Filtering ASVs based on dissimilarity across sample replicates
Here we’ll use the Bray-Curtis index to identify sample replicates (within each locus) that are more dissimilar than similar to the other replicates. Dissimilarity can be an indication of an issue (contamination, etc.) with a particular replicate.
This uses the output from the species-occupancy detection modeling in 03-species-occupancy-model.Rmd The occupancy modeling uses the ASVs (not taxonomy) and I’ll use a similar approach here with the Bray-Curtis and NMDS analyses.
Process
The process is a bit cumbersome because it requires looking at each sample/locus/replicate for the full reference DNA pool and vouchered reference pool.
The process for looking at the dissimilarity among replicates is to: 1. Read in data that has been cleaned up using the occupancy modeling 2. Create a community matrix (per locus) 3. Standardize data across replicates (fct decostand) 4. Generate Bray-Curtis distances (fct vegdist) 4a. Are any replicates more dissimilar than similar? 5. Generate NMDS plots from distance matrix (fct metaMDS)
Outputs
Based on the NMDS plots and Bray-Curtis dissimilarity index, I generated a list of samples to remove:
../data/reference_pool_dissimilarity_samples_to_remove.csv
The data that were used to generate that list are output .csv files from the Bray-Curtis function, implemented below.
In addition, three loci had insufficient data across all 18 samples in both the vouchered and full reference pools to be included in these analyses and will be dropped from further analyses:
16Sfish teleo crust2
source("../R/metabarcoding-funcs.R")library(tidyverse)
library(stringi)
library(vegan)
library(reshape2)
library(textshape)
library(rlist)
# output from the ASV filtering based on the SODM for
# vouchered ref
vrp_sodm_filtered_df <- readRDS("../data/voucher_features_sodm_filtered_taxonomy_df.rds")
# full reference
frp_sodm_filtered_df <- readRDS("../data/full_reference_sodm_filtered_taxonomy_df.rds")
I have wrapped the Bray-Curis and NMDS up into a function called bray_nmds_complete which outputs a .csv file with the replicates that are > 0.49 dissimilar and generates an NMDS plot.
I’ll use that function with an lappy and the list of loci, since each locus will be analyzed separately.
To cycle over a list of the loci…
# grab the names of the loci from the full dataframe
locs <- frp_sodm_filtered_df %>%
select(locus) %>%
unique() %>%
as.list()
# turn that into a list that could be cycled over
loc_list <- locs$locus
# make a separate list for the VRP samples
locs19 <- frp_sodm_filtered_df %>%
select(locus) %>%
unique() %>%
filter(!locus %in% c("crust2", "16Sfish", "teleo")) %>%
as.list()
# turn that into a list that could be cycled over
loc_list19 <- locs19$locus
Full Reference dataframe
# cycle over the list of loci for the full reference pool sample replicates
# using the bray-curtis function to test for dissimilarity
lapply(loc_list19, bray_nmds_complete, sodm_filtered_df = frp_sodm_filtered_df, sample = "FRP")Run 0 stress 0.05032398
Run 1 stress 0.05032594
... Procrustes: rmse 0.001963745 max resid 0.004266198
... Similar to previous best
Run 2 stress 0.06433189
Run 3 stress 0.3209238
Run 4 stress 0.227495
Run 5 stress 0.05032713
... Procrustes: rmse 0.00111975 max resid 0.002597424
... Similar to previous best
Run 6 stress 0.05032779
... Procrustes: rmse 0.002633749 max resid 0.005649633
... Similar to previous best
Run 7 stress 0.06720142
Run 8 stress 0.3209238
Run 9 stress 0.06433195
Run 10 stress 0.06989063
Run 11 stress 0.102771
Run 12 stress 0.06433192
Run 13 stress 0.06720143
Run 14 stress 0.06989068
Run 15 stress 0.08181662
Run 16 stress 0.05033157
... Procrustes: rmse 0.003521328 max resid 0.007473747
... Similar to previous best
Run 17 stress 0.06433196
Run 18 stress 0.05032506
... Procrustes: rmse 0.0005089887 max resid 0.001183118
... Similar to previous best
Run 19 stress 0.06433186
Run 20 stress 0.05032567
... Procrustes: rmse 0.001884185 max resid 0.004092335
... Similar to previous best
*** Solution reached
Run 0 stress 0.05227481
Run 1 stress 0.1777184
Run 2 stress 0.07170935
Run 3 stress 0.1740507
Run 4 stress 0.07171101
Run 5 stress 0.05227457
... New best solution
... Procrustes: rmse 0.001858273 max resid 0.003812068
... Similar to previous best
Run 6 stress 0.03669723
... New best solution
... Procrustes: rmse 0.08285406 max resid 0.2056512
Run 7 stress 0.07170998
Run 8 stress 0.05227633
Run 9 stress 0.1672324
Run 10 stress 0.05227504
Run 11 stress 0.07170832
Run 12 stress 0.1955433
Run 13 stress 0.1777184
Run 14 stress 0.07171085
Run 15 stress 0.0522757
Run 16 stress 0.071711
Run 17 stress 0.05227607
Run 18 stress 0.07170828
Run 19 stress 0.07171016
Run 20 stress 0.1740537
Run 21 stress 0.03669809
... Procrustes: rmse 0.0004412054 max resid 0.0008091596
... Similar to previous best
*** Solution reached
Run 0 stress 0.001280727
Run 1 stress 0.0008851493
... New best solution
... Procrustes: rmse 0.02747565 max resid 0.05308799
Run 2 stress 9.499491e-05
... New best solution
... Procrustes: rmse 0.09213706 max resid 0.183262
Run 3 stress 9.897523e-05
... Procrustes: rmse 0.0002913263 max resid 0.0005779135
... Similar to previous best
Run 4 stress 0.0008187765
Run 5 stress 9.682415e-05
... Procrustes: rmse 0.05278958 max resid 0.1071393
Run 6 stress 9.846953e-05
... Procrustes: rmse 0.2255152 max resid 0.4222329
Run 7 stress 9.937463e-05
... Procrustes: rmse 0.2058249 max resid 0.3857322
Run 8 stress 9.804859e-05
... Procrustes: rmse 0.2103496 max resid 0.3940449
Run 9 stress 0.0001140746
... Procrustes: rmse 0.1326229 max resid 0.2521839
Run 10 stress 0.0005208338
... Procrustes: rmse 0.009388914 max resid 0.01818415
Run 11 stress 9.95845e-05
... Procrustes: rmse 0.1594821 max resid 0.3010649
Run 12 stress 9.792724e-05
... Procrustes: rmse 0.03589823 max resid 0.07242845
Run 13 stress 9.706015e-05
... Procrustes: rmse 0.1558765 max resid 0.2945659
Run 14 stress 0.000310356
... Procrustes: rmse 0.1014804 max resid 0.1951773
Run 15 stress 9.659121e-05
... Procrustes: rmse 0.06800617 max resid 0.1320285
Run 16 stress 9.92103e-05
... Procrustes: rmse 0.008701921 max resid 0.01726798
Run 17 stress 9.751976e-05
... Procrustes: rmse 0.2089696 max resid 0.3915145
Run 18 stress 0.001147709
Run 19 stress 9.972157e-05
... Procrustes: rmse 0.0579419 max resid 0.1178463
Run 20 stress 9.17396e-05
... New best solution
... Procrustes: rmse 0.002421848 max resid 0.004777992
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
some squared distances are negative and changed to zero
Run 0 stress 0.01793481
Run 1 stress 0.02377418
Run 2 stress 0.01793592
... Procrustes: rmse 0.0002903769 max resid 0.0006526605
... Similar to previous best
Run 3 stress 0.01793833
... Procrustes: rmse 0.0008104507 max resid 0.001786647
... Similar to previous best
Run 4 stress 0.02586193
Run 5 stress 0.2690221
Run 6 stress 0.01793677
... Procrustes: rmse 0.0004574407 max resid 0.001019185
... Similar to previous best
Run 7 stress 0.0306749
Run 8 stress 0.02377422
Run 9 stress 0.01793048
... New best solution
... Procrustes: rmse 0.002429503 max resid 0.005138497
... Similar to previous best
Run 10 stress 0.01793331
... Procrustes: rmse 0.001956373 max resid 0.004138439
... Similar to previous best
Run 11 stress 0.0179379
... Procrustes: rmse 0.003182547 max resid 0.006853465
... Similar to previous best
Run 12 stress 0.02585976
Run 13 stress 0.01793783
... Procrustes: rmse 0.003166088 max resid 0.006775573
... Similar to previous best
Run 14 stress 0.02864909
Run 15 stress 0.02377422
Run 16 stress 0.02377464
Run 17 stress 0.01793927
... Procrustes: rmse 0.00339453 max resid 0.007268699
... Similar to previous best
Run 18 stress 0.03067444
Run 19 stress 0.2190095
Run 20 stress 0.01793866
... Procrustes: rmse 0.003295913 max resid 0.007055757
... Similar to previous best
*** Solution reached
some squared distances are negative and changed to zero
Run 0 stress 0.1496671
Run 1 stress 0.1634708
Run 2 stress 0.1634708
Run 3 stress 0.1468143
... New best solution
... Procrustes: rmse 0.2448269 max resid 0.4339198
Run 4 stress 0.1535343
Run 5 stress 0.1535326
Run 6 stress 0.1537343
Run 7 stress 0.1596704
Run 8 stress 0.1811272
Run 9 stress 0.1536952
Run 10 stress 0.1570088
Run 11 stress 0.1496671
Run 12 stress 0.1537174
Run 13 stress 0.1535332
Run 14 stress 0.1468143
... New best solution
... Procrustes: rmse 7.581228e-07 max resid 1.057093e-06
... Similar to previous best
Run 15 stress 0.1941469
Run 16 stress 0.1894768
Run 17 stress 0.163471
Run 18 stress 0.1772823
Run 19 stress 0.1634708
Run 20 stress 0.1468143
... Procrustes: rmse 1.652641e-06 max resid 2.629501e-06
... Similar to previous best
*** Solution reached
Run 0 stress 0.07131921
Run 1 stress 0.185523
Run 2 stress 0.07071025
... New best solution
... Procrustes: rmse 0.06502016 max resid 0.1428037
Run 3 stress 0.1103686
Run 4 stress 0.07132007
Run 5 stress 0.07131933
Run 6 stress 0.07131936
Run 7 stress 0.07071025
... New best solution
... Procrustes: rmse 3.940693e-06 max resid 6.483427e-06
... Similar to previous best
Run 8 stress 0.3209238
Run 9 stress 0.07071025
... New best solution
... Procrustes: rmse 2.607509e-06 max resid 4.656192e-06
... Similar to previous best
Run 10 stress 0.1103686
Run 11 stress 0.1103687
Run 12 stress 0.07131969
Run 13 stress 0.1103686
Run 14 stress 0.1223463
Run 15 stress 0.07071025
... Procrustes: rmse 2.058157e-05 max resid 3.238398e-05
... Similar to previous best
Run 16 stress 0.07131985
Run 17 stress 0.07131958
Run 18 stress 0.1103687
Run 19 stress 0.07071026
... Procrustes: rmse 5.569717e-05 max resid 8.97981e-05
... Similar to previous best
Run 20 stress 0.1223413
*** Solution reached
Run 0 stress 0.03404271
Run 1 stress 0.04241063
Run 2 stress 0.04073004
Run 3 stress 0.05391961
Run 4 stress 0.05635849
Run 5 stress 0.05464615
Run 6 stress 0.03404193
... New best solution
... Procrustes: rmse 0.0004868161 max resid 0.0006450974
... Similar to previous best
Run 7 stress 0.04241149
Run 8 stress 0.04127956
Run 9 stress 0.05464688
Run 10 stress 0.05464741
Run 11 stress 0.04073003
Run 12 stress 0.04073009
Run 13 stress 0.05392019
Run 14 stress 0.05391934
Run 15 stress 0.05464615
Run 16 stress 0.03404373
... Procrustes: rmse 0.0007670957 max resid 0.001079974
... Similar to previous best
Run 17 stress 0.04072995
Run 18 stress 0.05464613
Run 19 stress 0.05635845
Run 20 stress 0.04073001
*** Solution reached
Run 0 stress 0.001593672
Run 1 stress 0.0004533559
... New best solution
... Procrustes: rmse 0.007094137 max resid 0.0130032
Run 2 stress 0.0008871839
... Procrustes: rmse 0.002653471 max resid 0.003735267
... Similar to previous best
Run 3 stress 9.946597e-05
... New best solution
... Procrustes: rmse 0.002142816 max resid 0.002976221
... Similar to previous best
Run 4 stress 9.305128e-05
... New best solution
... Procrustes: rmse 0.0004708507 max resid 0.0007991972
... Similar to previous best
Run 5 stress 9.299729e-05
... New best solution
... Procrustes: rmse 0.0001144739 max resid 0.0002248952
... Similar to previous best
Run 6 stress 0.1866276
Run 7 stress 0.1866276
Run 8 stress 9.636433e-05
... Procrustes: rmse 1.473294e-05 max resid 2.72295e-05
... Similar to previous best
Run 9 stress 0.1866276
Run 10 stress 9.539976e-05
... Procrustes: rmse 0.0001372894 max resid 0.0002256603
... Similar to previous best
Run 11 stress 0.0001514991
... Procrustes: rmse 0.0008454852 max resid 0.001399129
... Similar to previous best
Run 12 stress 7.740948e-05
... New best solution
... Procrustes: rmse 0.0001485035 max resid 0.0003484905
... Similar to previous best
Run 13 stress 0.0002026789
... Procrustes: rmse 0.001175126 max resid 0.001675374
... Similar to previous best
Run 14 stress 0.0002389813
... Procrustes: rmse 0.001398349 max resid 0.001986637
... Similar to previous best
Run 15 stress 0.0007600335
Run 16 stress 0.0009157349
Run 17 stress 0.001005354
Run 18 stress 0.0006401498
Run 19 stress 0.1866276
Run 20 stress 9.122697e-05
... Procrustes: rmse 0.0001720985 max resid 0.0003684408
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
some squared distances are negative and changed to zero
Run 0 stress 0.004849781
Run 1 stress 0.007793128
Run 2 stress 0.007779583
Run 3 stress 9.872685e-05
... New best solution
... Procrustes: rmse 0.04608516 max resid 0.08171449
Run 4 stress 0.2203411
Run 5 stress 0.004849842
Run 6 stress 0.007804921
Run 7 stress 0.007776096
Run 8 stress 0.007768048
Run 9 stress 0.007874874
Run 10 stress 0.004849765
Run 11 stress 0.2628288
Run 12 stress 9.856175e-05
... New best solution
... Procrustes: rmse 0.0001823488 max resid 0.0002860683
... Similar to previous best
Run 13 stress 0.3043874
Run 14 stress 0.0004672985
... Procrustes: rmse 0.001773592 max resid 0.003044729
... Similar to previous best
Run 15 stress 0.007808896
Run 16 stress 0.007787191
Run 17 stress 0.007784496
Run 18 stress 0.001954411
Run 19 stress 0.007782754
Run 20 stress 0.007784116
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.002725987
Run 1 stress 0.001598293
... New best solution
... Procrustes: rmse 0.008666246 max resid 0.01570875
Run 2 stress 0.002510566
Run 3 stress 9.887145e-05
... New best solution
... Procrustes: rmse 0.03239538 max resid 0.05894239
Run 4 stress 9.009163e-05
... New best solution
... Procrustes: rmse 0.0001627038 max resid 0.0002598752
... Similar to previous best
Run 5 stress 8.039583e-05
... New best solution
... Procrustes: rmse 9.294059e-05 max resid 0.0002149094
... Similar to previous best
Run 6 stress 9.346512e-05
... Procrustes: rmse 0.0001923068 max resid 0.0003924234
... Similar to previous best
Run 7 stress 0.0007114696
Run 8 stress 0.01220527
Run 9 stress 8.288297e-05
... Procrustes: rmse 0.0001455327 max resid 0.000279312
... Similar to previous best
Run 10 stress 0.0002002628
... Procrustes: rmse 0.004380793 max resid 0.008180704
... Similar to previous best
Run 11 stress 0.003540765
Run 12 stress 0.002632566
Run 13 stress 0.001345479
Run 14 stress 9.714506e-05
... Procrustes: rmse 0.0009914852 max resid 0.002052403
... Similar to previous best
Run 15 stress 0.007292963
Run 16 stress 0.0007634434
Run 17 stress 0.003274976
Run 18 stress 0.001888589
Run 19 stress 8.209626e-05
... Procrustes: rmse 0.0002077218 max resid 0.0005049695
... Similar to previous best
Run 20 stress 0.0007201802
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.007061937
Run 1 stress 0.006133232
... New best solution
... Procrustes: rmse 0.04020321 max resid 0.06360244
Run 2 stress 0.003945341
... New best solution
... Procrustes: rmse 0.04675964 max resid 0.07348764
Run 3 stress 0.003778913
... New best solution
... Procrustes: rmse 0.02050278 max resid 0.03255848
Run 4 stress 0.0004329439
... New best solution
... Procrustes: rmse 0.05334419 max resid 0.08268353
Run 5 stress 0.0004098361
... New best solution
... Procrustes: rmse 0.001820381 max resid 0.00284126
... Similar to previous best
Run 6 stress 0.006594832
Run 7 stress 0.001424179
Run 8 stress 0.0061523
Run 9 stress 0.001503611
Run 10 stress 0.00464189
Run 11 stress 0.00196111
Run 12 stress 0.00310235
Run 13 stress 0.005356668
Run 14 stress 0.0001327757
... New best solution
... Procrustes: rmse 0.004379381 max resid 0.00677173
... Similar to previous best
Run 15 stress 0.000516457
... Procrustes: rmse 0.006050742 max resid 0.009392071
Run 16 stress 0.003682546
Run 17 stress 0.003664024
Run 18 stress 0.006487141
Run 19 stress 0.0006784865
Run 20 stress 9.158779e-05
... New best solution
... Procrustes: rmse 0.001409623 max resid 0.002104411
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.0006167596
Run 1 stress 0.0007789301
... Procrustes: rmse 0.09172011 max resid 0.1769081
Run 2 stress 0.001121839
Run 3 stress 0.0008820109
... Procrustes: rmse 0.02945519 max resid 0.0741092
Run 4 stress 0.001202145
Run 5 stress 0.001281649
Run 6 stress 0.0008621738
... Procrustes: rmse 0.09580386 max resid 0.2495048
Run 7 stress 0.001745402
Run 8 stress 0.2517984
Run 9 stress 0.001728913
Run 10 stress 0.001715897
Run 11 stress 0.0003773019
... New best solution
... Procrustes: rmse 0.1020543 max resid 0.2116814
Run 12 stress 0.190385
Run 13 stress 0.002006578
Run 14 stress 9.597716e-05
... New best solution
... Procrustes: rmse 0.163036 max resid 0.3305894
Run 15 stress 0.0006464816
Run 16 stress 0.001721668
Run 17 stress 9.735888e-05
... Procrustes: rmse 0.1614917 max resid 0.3688607
Run 18 stress 0.0001726412
... Procrustes: rmse 0.03366803 max resid 0.07303108
Run 19 stress 0.001927828
Run 20 stress 0.0002863077
... Procrustes: rmse 0.03872929 max resid 0.0835279
Run 21 stress 9.993534e-05
... Procrustes: rmse 0.1279387 max resid 0.3522714
Run 22 stress 0.0006602949
Run 23 stress 9.937423e-05
... Procrustes: rmse 0.01826084 max resid 0.03797475
Run 24 stress 9.306018e-05
... New best solution
... Procrustes: rmse 0.1628553 max resid 0.3713916
Run 25 stress 0.001290327
Run 26 stress 0.000945505
Run 27 stress 0.002120838
Run 28 stress 9.245546e-05
... New best solution
... Procrustes: rmse 0.1556283 max resid 0.3070008
Run 29 stress 0.002042329
Run 30 stress 9.283865e-05
... Procrustes: rmse 0.1760775 max resid 0.3658075
Run 31 stress 0.0006070544
Run 32 stress 9.907401e-05
... Procrustes: rmse 0.09214861 max resid 0.2023489
Run 33 stress 9.099424e-05
... New best solution
... Procrustes: rmse 0.01350967 max resid 0.03286582
Run 34 stress 9.777701e-05
... Procrustes: rmse 0.1216854 max resid 0.3112685
Run 35 stress 0.0006025806
Run 36 stress 0.001194515
Run 37 stress 0.001263133
Run 38 stress 9.9449e-05
... Procrustes: rmse 0.1252961 max resid 0.2988486
Run 39 stress 9.949342e-05
... Procrustes: rmse 0.00778975 max resid 0.01943024
Run 40 stress 0.0003813559
... Procrustes: rmse 0.1336997 max resid 0.2686601
Run 41 stress 0.0002976847
... Procrustes: rmse 0.107867 max resid 0.2272832
Run 42 stress 0.0004135365
... Procrustes: rmse 0.1357839 max resid 0.3351115
Run 43 stress 0.001705086
Run 44 stress 0.190385
Run 45 stress 9.94936e-05
... Procrustes: rmse 0.1699359 max resid 0.338255
Run 46 stress 0.001252003
Run 47 stress 0.000952599
Run 48 stress 8.803094e-05
... New best solution
... Procrustes: rmse 0.02565628 max resid 0.0637466
Run 49 stress 0.0007158958
Run 50 stress 9.9366e-05
... Procrustes: rmse 0.1410323 max resid 0.2704096
*** No convergence -- monoMDS stopping criteria:
32: no. of iterations >= maxit
15: stress < smin
1: stress ratio > sratmax
2: scale factor of the gradient < sfgrminstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.08220736
Run 1 stress 0.1046338
Run 2 stress 0.08220815
... Procrustes: rmse 0.0005210259 max resid 0.000852318
... Similar to previous best
Run 3 stress 0.09077278
Run 4 stress 0.0822094
... Procrustes: rmse 0.001866474 max resid 0.003013214
... Similar to previous best
Run 5 stress 0.09077186
Run 6 stress 0.07644664
... New best solution
... Procrustes: rmse 0.2173407 max resid 0.4065968
Run 7 stress 0.0922239
Run 8 stress 0.07644676
... Procrustes: rmse 0.000196478 max resid 0.0004129595
... Similar to previous best
Run 9 stress 0.2382677
Run 10 stress 0.09077153
Run 11 stress 0.07644669
... Procrustes: rmse 0.0001142272 max resid 0.0002356965
... Similar to previous best
Run 12 stress 0.09803422
Run 13 stress 0.09077179
Run 14 stress 0.07644684
... Procrustes: rmse 0.0002418747 max resid 0.0005041906
... Similar to previous best
Run 15 stress 0.07644665
... Procrustes: rmse 2.050792e-05 max resid 3.960642e-05
... Similar to previous best
Run 16 stress 0.09077417
Run 17 stress 0.2007841
Run 18 stress 0.08221227
Run 19 stress 0.07644664
... Procrustes: rmse 3.7397e-06 max resid 7.186848e-06
... Similar to previous best
Run 20 stress 0.09785412
*** Solution reached
Run 0 stress 0.02704468
Run 1 stress 0.02704507
... Procrustes: rmse 0.0005381191 max resid 0.0007774085
... Similar to previous best
Run 2 stress 0.1111581
Run 3 stress 0.02704669
... Procrustes: rmse 0.001076435 max resid 0.001620683
... Similar to previous best
Run 4 stress 0.02704519
... Procrustes: rmse 0.0005815017 max resid 0.0008398243
... Similar to previous best
Run 5 stress 0.02704708
... Procrustes: rmse 0.001172974 max resid 0.001769932
... Similar to previous best
Run 6 stress 0.02704588
... Procrustes: rmse 0.0008172933 max resid 0.001239776
... Similar to previous best
Run 7 stress 0.1111585
Run 8 stress 0.02704598
... Procrustes: rmse 0.0008693736 max resid 0.001298837
... Similar to previous best
Run 9 stress 0.1097378
Run 10 stress 0.02704604
... Procrustes: rmse 0.0008909887 max resid 0.001330815
... Similar to previous best
Run 11 stress 0.02704449
... New best solution
... Procrustes: rmse 0.0002472625 max resid 0.0004381706
... Similar to previous best
Run 12 stress 0.02704766
... Procrustes: rmse 0.001093556 max resid 0.00171918
... Similar to previous best
Run 13 stress 0.02704643
... Procrustes: rmse 0.0008397852 max resid 0.001284364
... Similar to previous best
Run 14 stress 0.02704631
... Procrustes: rmse 0.0008500115 max resid 0.001320229
... Similar to previous best
Run 15 stress 0.1111587
Run 16 stress 0.02704679
... Procrustes: rmse 0.0009792526 max resid 0.0015229
... Similar to previous best
Run 17 stress 0.02704623
... Procrustes: rmse 0.0007882945 max resid 0.001232702
... Similar to previous best
Run 18 stress 0.02704598
... Procrustes: rmse 0.00070492 max resid 0.001108969
... Similar to previous best
Run 19 stress 0.02704445
... New best solution
... Procrustes: rmse 5.188721e-05 max resid 7.908923e-05
... Similar to previous best
Run 20 stress 0.02704602
... Procrustes: rmse 0.0008116506 max resid 0.001244635
... Similar to previous best
*** Solution reached
Run 0 stress 0.07320908
Run 1 stress 0.07320908
... Procrustes: rmse 2.004045e-06 max resid 4.218397e-06
... Similar to previous best
Run 2 stress 0.07320908
... Procrustes: rmse 1.734825e-06 max resid 3.710366e-06
... Similar to previous best
Run 3 stress 0.1761948
Run 4 stress 0.1711538
Run 5 stress 0.07320908
... Procrustes: rmse 2.441523e-06 max resid 5.217772e-06
... Similar to previous best
Run 6 stress 0.1457451
Run 7 stress 0.07320908
... Procrustes: rmse 1.23315e-06 max resid 2.397839e-06
... Similar to previous best
Run 8 stress 0.1783525
Run 9 stress 0.07320908
... Procrustes: rmse 9.256728e-07 max resid 1.292366e-06
... Similar to previous best
Run 10 stress 0.07320908
... Procrustes: rmse 4.301807e-06 max resid 9.728604e-06
... Similar to previous best
Run 11 stress 0.1596171
Run 12 stress 0.07320908
... Procrustes: rmse 1.932452e-06 max resid 4.214723e-06
... Similar to previous best
Run 13 stress 0.07320908
... Procrustes: rmse 1.539691e-06 max resid 3.252986e-06
... Similar to previous best
Run 14 stress 0.1761967
Run 15 stress 0.07320908
... Procrustes: rmse 1.327486e-06 max resid 3.304982e-06
... Similar to previous best
Run 16 stress 0.07320908
... Procrustes: rmse 9.971043e-07 max resid 1.797971e-06
... Similar to previous best
Run 17 stress 0.07320908
... Procrustes: rmse 6.469091e-06 max resid 1.234083e-05
... Similar to previous best
Run 18 stress 0.07320908
... Procrustes: rmse 1.150321e-06 max resid 2.414092e-06
... Similar to previous best
Run 19 stress 0.07320908
... Procrustes: rmse 1.063947e-06 max resid 1.704786e-06
... Similar to previous best
Run 20 stress 0.1761947
*** Solution reached
Run 0 stress 0.0003690946
Run 1 stress 0.2968929
Run 2 stress 9.913093e-05
... New best solution
... Procrustes: rmse 0.07085411 max resid 0.1516461
Run 3 stress 9.999722e-05
... Procrustes: rmse 0.0002201373 max resid 0.0004327531
... Similar to previous best
Run 4 stress 9.575975e-05
... New best solution
... Procrustes: rmse 0.0001794116 max resid 0.0004220792
... Similar to previous best
Run 5 stress 9.260103e-05
... New best solution
... Procrustes: rmse 0.0002044742 max resid 0.0003531156
... Similar to previous best
Run 6 stress 0.0001600694
... Procrustes: rmse 0.01505675 max resid 0.03167053
Run 7 stress 0.0001596279
... Procrustes: rmse 0.00032951 max resid 0.0006006541
... Similar to previous best
Run 8 stress 9.769899e-05
... Procrustes: rmse 3.782302e-05 max resid 6.067523e-05
... Similar to previous best
Run 9 stress 0.2796297
Run 10 stress 9.143806e-05
... New best solution
... Procrustes: rmse 6.578362e-05 max resid 0.0001321742
... Similar to previous best
Run 11 stress 0.001538226
Run 12 stress 9.724414e-05
... Procrustes: rmse 0.1357138 max resid 0.2768219
Run 13 stress 9.933341e-05
... Procrustes: rmse 0.06645189 max resid 0.1329136
Run 14 stress 9.924928e-05
... Procrustes: rmse 0.0002999558 max resid 0.0007423378
... Similar to previous best
Run 15 stress 9.589022e-05
... Procrustes: rmse 0.05518586 max resid 0.1180289
Run 16 stress 0.001564066
Run 17 stress 0.001468815
Run 18 stress 8.110974e-05
... New best solution
... Procrustes: rmse 0.0002767109 max resid 0.000640692
... Similar to previous best
Run 19 stress 9.550164e-05
... Procrustes: rmse 0.0001615734 max resid 0.0003296234
... Similar to previous best
Run 20 stress 9.425705e-05
... Procrustes: rmse 0.0002885959 max resid 0.0006592086
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.04781366
Run 1 stress 0.04663982
... New best solution
... Procrustes: rmse 0.2034987 max resid 0.4329019
Run 2 stress 0.04663972
... New best solution
... Procrustes: rmse 0.0001467378 max resid 0.0003408214
... Similar to previous best
Run 3 stress 0.05351554
Run 4 stress 0.05351514
Run 5 stress 0.04781326
Run 6 stress 0.04781314
Run 7 stress 0.04781331
Run 8 stress 0.0535149
Run 9 stress 0.04663969
... New best solution
... Procrustes: rmse 7.367476e-05 max resid 0.0001578297
... Similar to previous best
Run 10 stress 0.0466398
... Procrustes: rmse 0.0001488907 max resid 0.0002506899
... Similar to previous best
Run 11 stress 0.04781314
Run 12 stress 0.05351482
Run 13 stress 0.04663977
... Procrustes: rmse 0.0001342677 max resid 0.000256718
... Similar to previous best
Run 14 stress 0.05351515
Run 15 stress 0.04663976
... Procrustes: rmse 0.0001266586 max resid 0.000213622
... Similar to previous best
Run 16 stress 0.05351574
Run 17 stress 0.04781315
Run 18 stress 0.04663972
... Procrustes: rmse 8.51421e-05 max resid 0.0001712532
... Similar to previous best
Run 19 stress 0.04781349
Run 20 stress 0.04663991
... Procrustes: rmse 0.0002006478 max resid 0.0004887694
... Similar to previous best
*** Solution reached
Run 0 stress 0.03852861
Run 1 stress 0.1654582
Run 2 stress 0.03852939
... Procrustes: rmse 0.0004331954 max resid 0.001020602
... Similar to previous best
Run 3 stress 0.03852895
... Procrustes: rmse 0.0002270687 max resid 0.0005334849
... Similar to previous best
Run 4 stress 0.0385288
... Procrustes: rmse 0.0006556131 max resid 0.001548393
... Similar to previous best
Run 5 stress 0.03852894
... Procrustes: rmse 0.0007260868 max resid 0.001713027
... Similar to previous best
Run 6 stress 0.03852912
... Procrustes: rmse 0.0003170953 max resid 0.000746315
... Similar to previous best
Run 7 stress 0.03852889
... Procrustes: rmse 0.0002084362 max resid 0.0004895812
... Similar to previous best
Run 8 stress 0.03852895
... Procrustes: rmse 0.0002429794 max resid 0.000571497
... Similar to previous best
Run 9 stress 0.2316853
Run 10 stress 0.03852916
... Procrustes: rmse 0.0003395288 max resid 0.0007998688
... Similar to previous best
Run 11 stress 0.0385288
... Procrustes: rmse 0.0001544866 max resid 0.0003631234
... Similar to previous best
Run 12 stress 0.1573475
Run 13 stress 0.03852853
... New best solution
... Procrustes: rmse 8.128728e-05 max resid 0.0001926985
... Similar to previous best
Run 14 stress 0.0385286
... Procrustes: rmse 8.637044e-05 max resid 0.0002037003
... Similar to previous best
Run 15 stress 0.03852865
... Procrustes: rmse 0.0001313458 max resid 0.0003102947
... Similar to previous best
Run 16 stress 0.03852888
... Procrustes: rmse 0.0002692969 max resid 0.0006361657
... Similar to previous best
Run 17 stress 0.03852901
... Procrustes: rmse 0.0003519962 max resid 0.000831036
... Similar to previous best
Run 18 stress 0.301734
Run 19 stress 0.03852936
... Procrustes: rmse 0.0005046 max resid 0.001191245
... Similar to previous best
Run 20 stress 0.03852861
... Procrustes: rmse 4.364481e-05 max resid 9.68068e-05
... Similar to previous best
*** Solution reached
Run 0 stress 0.004375477
Run 1 stress 0.2392124
Run 2 stress 0.004386192
... Procrustes: rmse 0.001463297 max resid 0.002544894
... Similar to previous best
Run 3 stress 0.2944258
Run 4 stress 0.004437502
... Procrustes: rmse 0.006321878 max resid 0.0082149
Run 5 stress 0.004428057
... Procrustes: rmse 0.005960111 max resid 0.008000272
Run 6 stress 0.04726353
Run 7 stress 0.004389588
... Procrustes: rmse 0.003529055 max resid 0.004949438
... Similar to previous best
Run 8 stress 0.05574174
Run 9 stress 0.202569
Run 10 stress 0.004390746
... Procrustes: rmse 0.001845977 max resid 0.003198968
... Similar to previous best
Run 11 stress 0.04258046
Run 12 stress 0.004447288
... Procrustes: rmse 0.006643638 max resid 0.008701654
Run 13 stress 0.004374636
... New best solution
... Procrustes: rmse 0.0003986833 max resid 0.0005540125
... Similar to previous best
Run 14 stress 0.04726461
Run 15 stress 0.00464466
... Procrustes: rmse 0.009726585 max resid 0.01382343
Run 16 stress 0.04257692
Run 17 stress 0.004386292
... Procrustes: rmse 0.001850264 max resid 0.0030073
... Similar to previous best
Run 18 stress 0.04258072
Run 19 stress 0.00438586
... Procrustes: rmse 0.002681347 max resid 0.003977501
... Similar to previous best
Run 20 stress 0.05574241
*** Solution reached
[[1]]
[[1]][[1]]
$sites
PCoA1 PCoA2
FRP_3_2 -0.0077556760 -0.0004483978
FRP_1_1 -0.0074078032 0.0106175215
FRP_1_2 0.0136031448 -0.0045690012
FRP_1_3 -0.0003200055 -0.0033346282
FRP_2_1 -0.0084371322 -0.0055360574
FRP_2_2 -0.0114169252 -0.0009201659
FRP_2_3 0.0015782355 -0.0005754210
FRP_3_1 0.0138635685 0.0065993296
FRP_3_3 0.0062925933 -0.0018331796
$centroids
PCoA1 PCoA2
1 0.0004802225 -1.930358e-03
2 -0.0076432259 -2.570950e-03
3 0.0055992833 8.032607e-05
attr(,"class")
[1] "ordiplot"
[[1]][[2]]
[[1]][[2]]$x
[1] 0.013431725 0.022975729 0.013386603 0.012024594 0.009644468 0.011296132 0.024177681
[8] 0.017863794 0.026378430 0.016655836 0.017323198 0.012602273 0.017200114 0.021926298
[15] 0.020100664 0.016227316 0.024348019 0.025619571 0.016398915 0.013476611 0.014177795
[22] 0.010969808 0.012970100 0.012118562 0.017715952 0.013157313 0.011247205 0.017141118
[29] 0.025668067 0.017769823 0.016486741 0.027339705 0.019960160 0.017643101 0.012066248
[36] 0.014492783
[[1]][[2]]$y
[1] 0.010427283 0.032887161 0.011820674 0.011360892 0.004583008 0.014402034 0.033000873
[8] 0.023190655 0.038356293 0.020785527 0.021514005 0.012368640 0.018327827 0.035162820
[15] 0.030117317 0.022600190 0.033659999 0.036596057 0.020028630 0.011985196 0.010509155
[22] 0.011611776 0.014534156 0.010184293 0.026005759 0.012219686 0.009717914 0.020447567
[29] 0.037578657 0.023152242 0.018816894 0.037401429 0.026545530 0.018600035 0.012648339
[36] 0.017118223
[[1]][[2]]$yf
[1] 0.012041850 0.033677713 0.012041850 0.012041850 0.004583008 0.012041850 0.033677713
[8] 0.024116219 0.037878861 0.020140084 0.020140084 0.012041850 0.020140084 0.033677713
[15] 0.030117317 0.020140084 0.033677713 0.036596057 0.020140084 0.012041850 0.012041850
[22] 0.010664845 0.012041850 0.012041850 0.024116219 0.012041850 0.010664845 0.020140084
[29] 0.037578657 0.024116219 0.020140084 0.037878861 0.026545530 0.020140084 0.012041850
[36] 0.017118223
[[1]][[3]]
[[2]]
[[2]][[1]]
$sites
PCoA1 PCoA2
FRP_1_2 0.06494987 -0.06626920
FRP_1_3 -0.17107055 -0.13782173
FRP_2_1 0.01742536 -0.06481453
FRP_2_2 0.04168515 -0.15435207
FRP_2_3 0.05092583 0.06977421
FRP_3_1 0.31688597 0.14104534
FRP_3_2 0.14193101 -0.01935849
FRP_3_3 -0.28249217 0.15091566
FRP_1_1 -0.18024048 0.08088081
$centroids
PCoA1 PCoA2
1 -0.09805807 -0.03627434
2 0.03708432 -0.06862697
3 0.10747934 0.05871270
attr(,"class")
[1] "ordiplot"
[[2]][[2]]
[[2]][[2]]$x
[1] 0.3770429 0.2461778 0.2934774 0.3566584 0.4025635 0.2909018 0.4530425 0.3557978 0.3540150
[10] 0.3437761 0.4104616 0.5734886 0.4657150 0.3736381 0.3588538 0.2848001 0.3572875 0.4293202
[19] 0.3009628 0.4119583 0.3378513 0.3017814 0.4573734 0.3366396 0.4783606 0.3883292 0.4013016
[28] 0.3570193 0.4361997 0.3638602 0.3948414 0.6182536 0.5559321 0.5127856 0.3987264 0.2624794
[[2]][[2]]$y
[1] 0.334923890 0.005658642 0.140255494 0.340264245 0.531499714 0.178170573 0.536509313
[8] 0.383522919 0.329268820 0.398875287 0.550190144 0.866367654 0.512160068 0.350756245
[15] 0.318521286 0.141810879 0.341973484 0.537157960 0.183806244 0.532034888 0.379916624
[22] 0.200197848 0.512105206 0.207560446 0.499398350 0.323561187 0.536326572 0.350085330
[29] 0.525503008 0.347697515 0.354759139 1.009084275 0.829126316 0.693654514 0.525116058
[36] 0.182186706
[[2]][[2]]$yf
[1] 0.349947236 0.005658642 0.160605913 0.349947236 0.527288522 0.160605913 0.527288522
[8] 0.349947236 0.349947236 0.349947236 0.527288522 0.866367654 0.527288522 0.349947236
[15] 0.349947236 0.160605913 0.349947236 0.527288522 0.183806244 0.527288522 0.349947236
[22] 0.200197848 0.527288522 0.207560446 0.527288522 0.349947236 0.527288522 0.349947236
[29] 0.527288522 0.349947236 0.354759139 1.009084275 0.829126316 0.693654514 0.525116058
[36] 0.160605913
[[2]][[3]]
[[3]]
[[3]][[1]]
$sites
PCoA1 PCoA2
FRP_2_2 -0.0056747798 0.017442242
FRP_3_1 -0.0056845971 0.008868028
FRP_1_3 0.0000209112 -0.018369993
FRP_1_2 0.0177420762 -0.023964050
FRP_1_1 -0.0199796633 -0.033721821
FRP_2_1 -0.0132891435 -0.005679593
FRP_2_3 -0.0095849868 -0.002671528
FRP_3_2 -0.0589465487 0.037203580
FRP_3_3 0.0953967317 0.020893134
$centroids
PCoA1 PCoA2
1 -0.0005652555 -0.0240508147
2 -0.0100271030 0.0004877264
3 -0.0045067655 0.0114597151
attr(,"class")
[1] "ordiplot"
[[3]][[2]]
[[3]][[2]]$x
[1] 0.05091691 0.05590369 0.06797155 0.06567495 0.05526485 0.05059249 0.07503465 0.10823322
[9] 0.05284606 0.06149564 0.06280045 0.05829094 0.04529058 0.07657186 0.10925392 0.04760468
[17] 0.04780922 0.05436990 0.04867337 0.08710807 0.10712747 0.05919926 0.07133588 0.06231871
[25] 0.10158450 0.09683261 0.05873039 0.05624024 0.08593452 0.12899995 0.03647458 0.08302039
[33] 0.11866578 0.07924674 0.11292312 0.15642901
[[3]][[2]]$y
[1] 1.557600e-05 3.329966e-05 5.940920e-05 4.957679e-05 2.900777e-05 1.318555e-05
[7] 9.844787e-02 9.852615e-02 2.162918e-05 4.643252e-05 4.157737e-05 2.827331e-05
[13] 1.707781e-05 9.846189e-02 9.853335e-02 2.617719e-05 2.127856e-05 2.171337e-05
[19] 2.484331e-05 9.848101e-02 9.852379e-02 2.279351e-05 4.276256e-05 5.059855e-05
[25] 9.850718e-02 9.852446e-02 2.464809e-05 3.759857e-05 9.849275e-02 9.850640e-02
[31] 1.582388e-05 9.846810e-02 9.850596e-02 9.845696e-02 9.851686e-02 1.372496e-01
[[3]][[2]]$yf
[1] 2.021212e-05 2.932263e-05 5.108588e-05 4.957679e-05 2.900777e-05 2.021212e-05
[7] 9.844787e-02 9.851875e-02 2.162918e-05 4.620281e-05 4.620281e-05 2.932263e-05
[13] 1.707781e-05 9.845942e-02 9.851875e-02 2.021212e-05 2.021212e-05 2.171337e-05
[19] 2.021212e-05 9.848688e-02 9.851875e-02 2.932263e-05 5.108588e-05 4.620281e-05
[25] 9.851582e-02 9.851582e-02 2.932263e-05 2.932263e-05 9.848688e-02 9.851875e-02
[31] 1.582388e-05 9.846810e-02 9.851875e-02 9.845942e-02 9.851875e-02 1.372496e-01
[[3]][[3]]
[[4]]
[[4]][[1]]
$sites
PCoA1 PCoA2
FRP_2_2 -0.262240453 -0.0038533877
FRP_3_1 0.008729208 0.2002859672
FRP_2_1 -0.173286965 0.0947070670
FRP_2_3 -0.056933156 0.0339735572
FRP_1_2 0.411606057 -0.1217504500
FRP_3_2 -0.263052267 -0.1718486962
FRP_3_3 0.460902494 0.0289761450
FRP_1_1 -0.117304324 -0.0608939723
FRP_1_3 -0.008420595 0.0004037698
$centroids
PCoA1 PCoA2
1 -0.003826581 -0.009450722
2 -0.151869651 0.051668726
3 0.028573925 0.131970064
attr(,"class")
[1] "ordiplot"
[[4]][[2]]
[[4]][[2]]$x
[1] 0.3666786 0.2745743 0.2846767 0.6936960 0.2460870 0.7395843 0.3220790 0.3384186 0.2934343
[10] 0.2606911 0.5440963 0.4580087 0.4636392 0.3434786 0.2499468 0.1881074 0.6220386 0.3746198
[19] 0.6702217 0.1862354 0.2540122 0.5142405 0.3486079 0.5204338 0.1581332 0.1529300 0.7029519
[28] 0.1684395 0.5477143 0.4507136 0.7471961 0.2733190 0.3668404 0.6078074 0.4970476 0.1677923
[[4]][[2]]$y
[1] 0.6316655 0.3277121 0.3825655 1.3261435 0.3210455 1.3827627 0.3179736 0.4917713 0.3343206
[10] 0.3714421 0.9791760 0.8521754 0.9008778 0.4885665 0.3163162 0.3051013 1.2069735 0.6118285
[19] 1.1910199 0.3564847 0.3602581 0.9547932 0.5036826 1.0004253 0.1209086 0.1116373 1.3048853
[28] 0.3219594 1.0098201 0.8599778 1.4340853 0.3852232 0.6060120 1.0859949 0.8912121 0.2211410
[[4]][[2]]$yf
[1] 0.6165020 0.3542136 0.3542136 1.3155144 0.3247369 1.3827627 0.3542136 0.4901689 0.3542136
[10] 0.3542136 0.9898007 0.8560766 0.8960449 0.4901689 0.3247369 0.3247369 1.1989967 0.6165020
[19] 1.1989967 0.3247369 0.3542136 0.9547932 0.5036826 0.9898007 0.1209086 0.1116373 1.3155144
[28] 0.3219594 1.0098201 0.8560766 1.4340853 0.3542136 0.6165020 1.0859949 0.8960449 0.2211410
[[4]][[3]]
[[5]]
[[5]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 -0.04014545 0.01465985
FRP_1_3 0.09254271 -0.03301385
FRP_2_1 -0.03086299 -0.02900160
FRP_2_2 -0.03078452 -0.11866051
FRP_2_3 -0.06272215 -0.01747867
FRP_3_1 0.02047142 0.11706061
FRP_3_2 -0.10791489 0.02973555
FRP_1_2 0.14426116 -0.01350986
FRP_3_3 0.01515471 0.05020848
$centroids
PCoA1 PCoA2
1 0.08707240 -0.02117427
2 -0.05221464 -0.03602501
3 -0.01946476 0.06400382
attr(,"class")
[1] "ordiplot"
[[5]][[2]]
[[5]][[2]]$x
[1] 0.1883248 0.2004467 0.1989875 0.1351847 0.2161442 0.1576516 0.2252707 0.0962406 0.1687482
[10] 0.1823747 0.1696022 0.1996427 0.2241094 0.1154127 0.1124088 0.1934365 0.1220679 0.2061328
[19] 0.1790426 0.2313514 0.1690148 0.1168174 0.2464477 0.1688671 0.2074800 0.2053333 0.1738575
[28] 0.0711903 0.2102079 0.0945083 0.1679886 0.1947591 0.1395905 0.2599633 0.1352807 0.1557269
[[5]][[2]]$y
[1] 0.16365380 0.21766030 0.10640470 0.13874779 0.28312227 0.22490608 0.26583439 0.09902492
[9] 0.19589003 0.23199901 0.18075942 0.17382419 0.27612345 0.10576822 0.08049805 0.18291730
[17] 0.08823767 0.12849952 0.11207748 0.27108802 0.15253616 0.09649341 0.28956095 0.13974590
[25] 0.33749225 0.15166241 0.19535845 0.09955983 0.27859812 0.10874032 0.24026448 0.19568789
[33] 0.18760538 0.36751655 0.20801396 0.18582984
[[5]][[2]]$yf
[1] 0.1787648 0.1787648 0.1787648 0.1387478 0.2853764 0.1787648 0.2853764 0.0969032 0.1787648
[10] 0.1787648 0.1787648 0.1787648 0.2853764 0.0969032 0.0969032 0.1787648 0.0969032 0.1787648
[19] 0.1787648 0.2853764 0.1787648 0.0969032 0.2895609 0.1787648 0.2853764 0.1787648 0.1787648
[28] 0.0969032 0.2853764 0.0969032 0.1787648 0.1787648 0.1787648 0.3675166 0.1787648 0.1787648
[[5]][[3]]
[[6]]
[[6]][[1]]
$sites
PCoA1 PCoA2
FRP_3_3 -0.008256521 0.002439797
FRP_2_2 0.042079766 -0.022582048
FRP_1_1 -0.098491142 0.005826303
FRP_2_1 0.022435380 0.042716838
FRP_1_3 0.003608971 -0.014881121
FRP_2_3 0.061202512 0.009883980
FRP_3_1 0.018025745 -0.041081332
FRP_1_2 -0.006717833 0.050579740
FRP_3_2 -0.033886879 -0.032902156
$centroids
PCoA1 PCoA2
1 -0.023867074 0.01500425
2 0.045217987 0.00856103
3 -0.008985759 -0.02340007
attr(,"class")
[1] "ordiplot"
[[6]][[2]]
[[6]][[2]]$x
[1] 0.08073536 0.10557947 0.06776137 0.08273844 0.09263127 0.08021865 0.09759218 0.07580858
[9] 0.14715290 0.08704157 0.08109290 0.06877224 0.06375325 0.11020774 0.10095889 0.13460894
[17] 0.12256326 0.16325352 0.13366212 0.12280966 0.09710267 0.09389212 0.07589208 0.10339667
[25] 0.09201891 0.10769727 0.09610167 0.06800812 0.09091154 0.08692299 0.08550895 0.10504501
[33] 0.11432958 0.10362410 0.07948290 0.10897734
[[6]][[2]]$y
[1] 0.04406408 0.13661181 0.06293692 0.02597394 0.07365702 0.03822742 0.09246097 0.06132521
[9] 0.17521642 0.07087068 0.06876656 0.04545737 0.03235644 0.12705362 0.08744182 0.18482501
[17] 0.12382793 0.21023192 0.14893955 0.14976532 0.09409409 0.06222172 0.05386229 0.09101813
[25] 0.07425352 0.12358736 0.09018412 0.06296215 0.06940291 0.06725038 0.07742249 0.12659250
[33] 0.12924799 0.13068753 0.05722104 0.13077936
[[6]][[2]]$yf
[1] 0.05207970 0.12854851 0.05207970 0.05207970 0.07072553 0.05207970 0.09125375 0.05207970
[9] 0.18002072 0.07072553 0.05207970 0.05207970 0.03235644 0.12854851 0.09125375 0.18002072
[17] 0.12854851 0.21023192 0.14935244 0.14935244 0.09125375 0.07072553 0.05207970 0.09125375
[25] 0.07072553 0.12854851 0.09018412 0.05207970 0.07072553 0.07072553 0.07072553 0.12854851
[33] 0.12854851 0.12854851 0.05207970 0.12854851
[[6]][[3]]
[[7]]
[[7]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 0.018644224 0.050111296
FRP_1_2 -0.116287721 0.026197492
FRP_1_3 -0.022436272 0.039460893
FRP_2_1 -0.086938562 -0.057004098
FRP_2_2 -0.006337469 -0.015211065
FRP_2_3 0.039072086 -0.021516388
FRP_3_1 0.037057588 -0.010721903
FRP_3_2 0.060726713 -0.003104382
FRP_3_3 0.076499412 -0.008211845
$centroids
PCoA1 PCoA2
1 -0.028483792 0.039471876
2 -0.006610574 -0.018272896
3 0.061086054 -0.007061574
attr(,"class")
[1] "ordiplot"
[[7]][[2]]
[[7]][[2]]$x
[1] 0.15408060 0.09098169 0.15403651 0.09542980 0.10571582 0.09943907 0.08278124 0.10682108
[9] 0.11057966 0.10751800 0.12893625 0.16836227 0.16625181 0.18510476 0.19938865 0.12828454
[17] 0.08236546 0.10880524 0.09870944 0.10932608 0.11684214 0.11152001 0.15047559 0.14527013
[25] 0.16122280 0.17699655 0.06838509 0.08789122 0.08882719 0.10182858 0.08537543 0.06656415
[33] 0.07512382 0.06827236 0.06488493 0.05333727
[[7]][[2]]$y
[1] 0.23580584 0.08657349 0.23432661 0.09129396 0.11079032 0.07513840 0.06039865 0.10898145
[9] 0.15421236 0.11537462 0.19294183 0.25356560 0.23723003 0.26836012 0.29742812 0.15111241
[17] 0.05517059 0.11551657 0.08894267 0.11461235 0.14881890 0.15469619 0.19851028 0.19904974
[25] 0.24015551 0.25088354 0.06261595 0.04618270 0.08553814 0.10490566 0.03625415 0.06631601
[33] 0.05324613 0.04278573 0.06048318 0.04871463
[[7]][[2]]$yf
[1] 0.23580584 0.08549733 0.23432661 0.08549733 0.10988588 0.08549733 0.05371701 0.10988588
[9] 0.15220997 0.11516785 0.19294183 0.25222457 0.23869277 0.26836012 0.29742812 0.15220997
[17] 0.05371701 0.11516785 0.08549733 0.11516785 0.15220997 0.15220997 0.19878001 0.19878001
[25] 0.23869277 0.25222457 0.05371701 0.05371701 0.08549733 0.10490566 0.05371701 0.05371701
[33] 0.05371701 0.05371701 0.05371701 0.04871463
[[7]][[3]]
[[8]]
[[8]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 0.05330609 -0.031014795
FRP_1_2 0.05474506 -0.020998469
FRP_1_3 0.02379525 -0.043544199
FRP_2_1 0.02893802 0.043458186
FRP_2_2 -0.05393802 0.001767947
FRP_2_3 0.04937047 0.040515655
FRP_3_1 -0.08813066 0.004220599
FRP_3_2 -0.09929917 -0.006695155
FRP_3_3 0.03121296 0.012290231
$centroids
PCoA1 PCoA2
1 0.04550140 -0.0312197924
2 0.02081394 0.0354897891
3 -0.07486700 0.0009467908
attr(,"class")
[1] "ordiplot"
[[8]][[2]]
[[8]][[2]]$x
[1] 0.07192330 0.07909866 0.10047336 0.13340879 0.08861081 0.15638693 0.16261143 0.07817981
[9] 0.08468035 0.09322242 0.13396872 0.09049408 0.15617428 0.16529537 0.08010778 0.09772089
[17] 0.11668041 0.10398264 0.13624896 0.14364076 0.09561981 0.11584932 0.07673165 0.13663881
[25] 0.15200740 0.08272309 0.13466223 0.09774362 0.09384041 0.11724206 0.15361650 0.16253229
[33] 0.07873143 0.07067902 0.13978029 0.14176573
[[8]][[2]]$y
[1] 8.261376e-07 4.574570e-05 4.103076e-05 1.209939e-01 3.917155e-05 1.210414e-01
[7] 1.210478e-01 5.337341e-05 4.535812e-05 4.116155e-05 1.209937e-01 3.836345e-05
[13] 1.210412e-01 1.210476e-01 5.266326e-05 2.787889e-05 1.209497e-01 5.104103e-05
[19] 1.209971e-01 1.210036e-01 2.753982e-05 1.209560e-01 6.587051e-05 1.210035e-01
[25] 1.210099e-01 5.379911e-05 1.209926e-01 4.761477e-05 5.389795e-05 1.209566e-01
[31] 1.210400e-01 1.210465e-01 3.596993e-05 7.064322e-06 1.210041e-01 1.210105e-01
[[8]][[2]]$yf
[1] 3.945230e-06 4.462925e-05 4.462925e-05 1.209934e-01 4.462925e-05 1.210414e-01
[7] 1.210477e-01 4.462925e-05 4.462925e-05 4.462925e-05 1.209934e-01 4.462925e-05
[13] 1.210412e-01 1.210477e-01 4.462925e-05 4.462925e-05 1.209528e-01 5.104103e-05
[19] 1.209971e-01 1.210070e-01 4.462925e-05 1.209528e-01 4.462925e-05 1.210035e-01
[25] 1.210099e-01 4.462925e-05 1.209934e-01 4.462925e-05 4.462925e-05 1.209566e-01
[31] 1.210400e-01 1.210465e-01 4.462925e-05 3.945230e-06 1.210041e-01 1.210070e-01
[[8]][[3]]
[[9]]
[[9]][[1]]
$sites
PCoA1 PCoA2
FRP_2_2 -0.012903642 0.0033319266
FRP_1_1 -0.024343127 0.0059714816
FRP_2_3 0.005336265 -0.0063422706
FRP_1_2 0.030020546 0.0093749670
FRP_1_3 0.002556233 -0.0035074582
FRP_3_3 0.011697789 -0.0112489763
FRP_3_1 0.019047681 0.0032600475
FRP_2_1 -0.012233598 0.0004484654
FRP_3_2 -0.019178147 -0.0012881829
$centroids
PCoA1 PCoA2
1 0.002556233 -0.0035074542
2 -0.010207025 0.0008571281
3 0.009758724 -0.0052784397
attr(,"class")
[1] "ordiplot"
[[9]][[2]]
[[9]][[2]]$x
[1] 0.012249502 0.022377459 0.043543925 0.017289068 0.028541047 0.032797207 0.009234898
[8] 0.015103742 0.034245755 0.055398344 0.028871185 0.040328636 0.044595792 0.020421552
[15] 0.019143236 0.030282660 0.009063522 0.015379388 0.019250908 0.023057360 0.026724602
[22] 0.030388353 0.028798673 0.016001443 0.044216609 0.051210767 0.012225053 0.019307238
[29] 0.017510125 0.024672870 0.018954241 0.029157544 0.036132457 0.033359628 0.040166419
[36] 0.015377484
[[9]][[2]]$y
[1] 2.728459e-02 2.729928e-02 7.463239e-02 2.729609e-02 5.272559e-02 5.274842e-02
[7] 1.915832e-05 2.728667e-02 5.277094e-02 1.019168e-01 5.276588e-02 7.463815e-02
[13] 7.944511e-02 2.728618e-02 2.729432e-02 5.275088e-02 8.324205e-06 2.729816e-02
[19] 2.729797e-02 2.730735e-02 3.871991e-02 5.275856e-02 5.271996e-02 2.729788e-02
[25] 7.463072e-02 9.147078e-02 2.729708e-02 2.730457e-02 2.730416e-02 3.871223e-02
[31] 2.729785e-02 5.273789e-02 5.286928e-02 5.275173e-02 6.547738e-02 2.730400e-02
[[9]][[2]]$yf
[1] 2.728945e-02 2.729928e-02 7.463375e-02 2.729812e-02 5.272277e-02 5.275291e-02
[7] 1.915832e-05 2.728945e-02 5.277094e-02 1.019168e-01 5.275155e-02 7.463375e-02
[13] 7.944511e-02 2.729812e-02 2.729812e-02 5.275155e-02 8.324205e-06 2.729812e-02
[19] 2.729812e-02 2.730735e-02 3.871991e-02 5.275291e-02 5.272277e-02 2.729812e-02
[25] 7.463375e-02 9.147078e-02 2.728945e-02 2.729812e-02 2.729812e-02 3.871223e-02
[31] 2.729812e-02 5.275155e-02 5.286928e-02 5.275291e-02 6.547738e-02 2.729812e-02
[[9]][[3]]
[[10]]
[[10]][[1]]
$sites
PCoA1 PCoA2
FRP_2_3 -0.1129215 -0.0235242886
FRP_3_1 -0.1085090 -0.0926596305
FRP_3_2 -0.1109232 -0.0673314110
FRP_1_1 -0.1098511 0.0698295568
FRP_2_1 -0.1119639 -0.0485883296
FRP_1_2 0.8862394 -0.0004000677
FRP_1_3 -0.1061476 0.1144883837
FRP_2_2 -0.1127645 0.0283004742
FRP_3_3 -0.1131584 0.0198853127
$centroids
PCoA1 PCoA2
1 -0.08319139 0.08974263
2 -0.11279088 -0.02261110
3 -0.11073208 -0.06478154
attr(,"class")
[1] "ordiplot"
[[10]][[2]]
[[10]][[2]]$x
[1] 0.07896193 0.05253035 0.10571999 0.03899107 0.99966198 0.14311035 0.06060667 0.04814131
[9] 0.04684927 0.16923263 0.06024814 0.99929467 0.21088097 0.12436663 0.11177748 0.14665749
[17] 0.03386601 0.99963411 0.18446158 0.10154417 0.08907881 0.12689191 0.99933964 0.08634292
[25] 0.05661381 0.05757869 0.99957339 0.16830648 0.08179215 0.06931322 0.99960286 0.99958696
[33] 0.99946317 0.09801482 0.09910349 0.01258915
[[10]][[2]]$y
[1] 0.20470314 0.11008698 0.20874640 0.10011176 877.11779827 0.25472219
[7] 0.17229728 0.15213436 0.09811550 0.27366930 0.10721820 877.00438316
[13] 0.18342433 0.28515148 0.26617767 0.24072377 0.03671387 877.07350870
[19] 0.21247561 0.23115184 0.20996577 0.20415966 876.93104898 0.15492892
[25] 0.06157179 0.06856141 877.04939491 0.18344158 0.19694596 0.17602868
[31] 876.86766147 876.98890678 876.99956613 0.20269417 0.19516103 0.02143671
[[10]][[2]]$yf
[1] 0.18552601 0.09843030 0.21994912 0.09843030 877.11779827 0.23377173
[7] 0.17229728 0.09843030 0.09843030 0.23377173 0.10721820 876.96771607
[13] 0.23377173 0.23377173 0.23377173 0.23377173 0.03671387 877.07350870
[19] 0.23377173 0.21994912 0.20260699 0.23377173 876.96771607 0.18552601
[25] 0.09843030 0.09843030 876.97638232 0.23377173 0.18552601 0.17602868
[31] 876.97638232 876.97638232 876.97638232 0.20260699 0.20260699 0.02143671
[[10]][[3]]
[[11]]
[[11]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 -0.09400627 -0.01329871
FRP_1_2 -0.06080563 0.02983990
FRP_1_3 -0.04081372 -0.02127699
FRP_2_1 -0.01763770 -0.02653275
FRP_2_2 -0.03687852 0.04266341
FRP_2_3 0.02357176 -0.02655387
FRP_3_1 0.24198995 0.02217142
FRP_3_2 0.04193813 -0.04371059
FRP_3_3 -0.05735799 0.03669819
$centroids
PCoA1 PCoA2
1 -0.063749272 0.005398960
2 -0.007845245 -0.007760707
3 0.044110954 -0.034511892
attr(,"class")
[1] "ordiplot"
[[11]][[2]]
[[11]][[2]]$x
[1] 0.08867492 0.11118395 0.12315747 0.12310010 0.15366852 0.34104496 0.15739338 0.10813631
[9] 0.08453847 0.09753411 0.09124153 0.12871589 0.30515101 0.14431388 0.07744923 0.09428018
[17] 0.12176223 0.11167290 0.29214634 0.13183991 0.10471197 0.10926224 0.09295979 0.27135258
[25] 0.10324325 0.10429229 0.10925194 0.29048895 0.13376635 0.10122935 0.23573331 0.08476898
[33] 0.13061640 0.21948618 0.30571728 0.14301322
[[11]][[2]]$y
[1] 2.309236e-04 4.449857e-04 5.131447e-04 3.991991e-04 6.801282e-04 3.832354e-01
[7] 8.223628e-04 2.334615e-04 2.490000e-04 2.824557e-04 2.563295e-04 4.653311e-04
[13] 3.830136e-01 5.930522e-04 2.161538e-05 2.162621e-04 4.240885e-04 4.476692e-04
[19] 3.828902e-01 4.815950e-04 2.333546e-04 2.966127e-04 2.322963e-04 3.827381e-01
[25] 3.122568e-04 2.830543e-04 3.318049e-04 3.828625e-01 5.245366e-04 2.762156e-04
[31] 3.825554e-01 2.101918e-04 4.739155e-04 3.824267e-01 3.830182e-01 5.949130e-04
[[11]][[2]]$yf
[1] 2.309236e-04 4.289856e-04 4.834966e-04 4.289856e-04 6.801282e-04 3.832354e-01
[7] 8.223628e-04 2.701331e-04 2.295959e-04 2.701331e-04 2.349626e-04 4.834966e-04
[13] 3.830136e-01 5.939826e-04 2.161538e-05 2.349626e-04 4.289856e-04 4.289856e-04
[19] 3.828902e-01 4.834966e-04 2.701331e-04 3.142088e-04 2.349626e-04 3.827381e-01
[25] 2.701331e-04 2.701331e-04 3.142088e-04 3.828625e-01 5.245366e-04 2.701331e-04
[31] 3.825554e-01 2.295959e-04 4.834966e-04 3.824267e-01 3.830182e-01 5.939826e-04
[[11]][[3]]
[[12]]
[[12]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 0.13633452 0.007020356
FRP_1_2 -0.07427683 0.090627628
FRP_1_3 -0.23293488 -0.063555514
FRP_2_1 -0.16906896 0.065042378
FRP_2_2 -0.21907658 -0.044549303
FRP_2_3 0.12276620 -0.005723485
FRP_3_1 0.15730028 -0.013551720
FRP_3_2 0.13831976 -0.003159585
FRP_3_3 0.14063649 -0.032150755
$centroids
PCoA1 PCoA2
1 -0.07020373 0.06086299
2 -0.15374948 0.02949032
3 0.14523099 -0.01419899
attr(,"class")
[1] "ordiplot"
[[12]][[2]]
[[12]][[2]]$x
[1] 0.25230432 0.38295668 0.32072753 0.37381292 0.10645175 0.11229274 0.09999688 0.13304752
[9] 0.22984910 0.15226335 0.21872760 0.23731514 0.27341607 0.25047448 0.25930873 0.17510279
[17] 0.11102898 0.36952033 0.40401055 0.38735462 0.39142903 0.13477951 0.31294109 0.34483294
[25] 0.32547392 0.34271947 0.35483586 0.38726032 0.36575812 0.37086130 0.10867488 0.09517648
[33] 0.12418441 0.10466003 0.13073032 0.12089383
[[12]][[2]]$y
[1] 0.3543938762 0.6082126426 0.3648138016 0.6079327052 0.0003874823 0.0004683584
[7] 0.0002460423 0.0007476549 0.3479555703 0.2710460504 0.3479340104 0.3540767465
[13] 0.3545840778 0.3543277032 0.3542058701 0.2710467481 0.0005179020 0.6080475045
[19] 0.6085898312 0.6082725608 0.6084076124 0.2706360709 0.3647420805 0.3652486332
[25] 0.3649317535 0.3651839900 0.6077678185 0.6083100927 0.6079927945 0.6081281924
[31] 0.0005472217 0.0002513606 0.0005171008 0.0003196526 0.0004802306 0.0005016682
[[12]][[2]]$yf
[1] 0.3543091498 0.6082126426 0.3648138016 0.6080361340 0.0003874823 0.0005054136
[7] 0.0002487015 0.0007476549 0.3479555703 0.2710460504 0.3479340104 0.3540767465
[13] 0.3545840778 0.3543091498 0.3543091498 0.2710467481 0.0005054136 0.6080361340
[19] 0.6085898312 0.6082913268 0.6084076124 0.2706360709 0.3647420805 0.3652486332
[25] 0.3649317535 0.3651839900 0.6077678185 0.6082913268 0.6079927945 0.6080361340
[31] 0.0005054136 0.0002487015 0.0005054136 0.0003196526 0.0005054136 0.0005054136
[[12]][[3]]
[[13]]
[[13]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 -0.040933368 0.012037860
FRP_1_2 -0.035049645 0.012805583
FRP_1_3 -0.034235234 -0.003442305
FRP_2_1 0.009620739 -0.008295548
FRP_2_2 0.014359868 -0.037189729
FRP_2_3 -0.001289886 -0.018053451
FRP_3_1 0.032747273 0.010376822
FRP_3_2 0.021816734 -0.002470293
FRP_3_3 0.032963520 0.034231061
$centroids
PCoA1 PCoA2
1 -0.036662371 0.007679577
2 0.007709566 -0.021308398
3 0.029977051 0.013699546
attr(,"class")
[1] "ordiplot"
[[13]][[2]]
[[13]][[2]]$x
[1] 0.06104226 0.06856393 0.07932263 0.08413225 0.07064816 0.08777414 0.08625987 0.08962218
[9] 0.06278358 0.07392153 0.08053554 0.07351484 0.07914690 0.08348338 0.08754436 0.06986980
[17] 0.07872013 0.07399851 0.08708987 0.08156579 0.08844205 0.06143118 0.06311144 0.06876200
[25] 0.06970861 0.06539897 0.06259994 0.06512319 0.07278045 0.08014720 0.07034222 0.07493446
[33] 0.07586844 0.06298123 0.05993611 0.07687521
[[13]][[2]]$y
[1] 0.01606697 0.02518159 0.04660328 0.04559271 0.03958380 0.06653044 0.05910220 0.07995054
[9] 0.01113316 0.03724560 0.04033046 0.03773078 0.05476687 0.04406416 0.06982057 0.04222320
[17] 0.04781195 0.04687470 0.05656817 0.04144700 0.07278461 0.01218069 0.02037843 0.02134685
[25] 0.02845840 0.03335028 0.00988722 0.03035252 0.04063731 0.03767527 0.04008920 0.04801302
[33] 0.04730013 0.02332879 0.01707774 0.03986392
[[13]][[2]]$yf
[1] 0.01326916 0.02755781 0.04497734 0.04559271 0.03958498 0.06817551 0.05783518 0.07995054
[9] 0.01326916 0.03958498 0.04497734 0.03958498 0.04497734 0.04497734 0.06817551 0.03958498
[17] 0.04497734 0.04497734 0.05783518 0.04497734 0.07278461 0.01326916 0.02185361 0.02755781
[25] 0.02845840 0.02755781 0.01326916 0.02755781 0.03958498 0.04497734 0.03958498 0.04497734
[33] 0.04497734 0.02185361 0.01326916 0.04497734
[[13]][[3]]
[[14]]
[[14]][[1]]
$sites
PCoA1 PCoA2
FRP_2_2 0.043097350 0.021621098
FRP_1_1 -0.039971382 0.015904363
FRP_1_2 0.024933783 -0.008642039
FRP_1_3 0.006557278 -0.019743956
FRP_2_1 0.011226499 0.001345905
FRP_2_3 0.012856685 0.015191099
FRP_3_2 -0.030369094 0.007631092
FRP_3_3 0.009631459 -0.025092552
FRP_3_1 -0.037962578 -0.008215009
$centroids
PCoA1 PCoA2
1 0.004484296 -0.010747992
2 0.017641163 0.011911074
3 -0.025621439 -0.004390609
attr(,"class")
[1] "ordiplot"
[[14]][[2]]
[[14]][[2]]$x
[1] 0.08574554 0.04431149 0.06150028 0.05317334 0.04728536 0.07875579 0.06075227 0.08845123
[9] 0.07293810 0.06312346 0.06032895 0.06235418 0.03453591 0.06897412 0.03428400 0.03970183
[17] 0.04228929 0.04262655 0.06631820 0.03910728 0.06630515 0.03729165 0.04398514 0.05495980
[25] 0.03380931 0.05392512 0.03060442 0.05548489 0.04121477 0.06001058 0.05131472 0.05054695
[33] 0.06248243 0.05472383 0.03510436 0.05745512
[[14]][[2]]$y
[1] 0.131068524 0.052617133 0.075554514 0.055900369 0.053004285 0.111206145 0.078647151
[8] 0.125564316 0.102483308 0.075941772 0.076308198 0.078227421 0.020736204 0.081617308
[15] 0.025353823 0.029283057 0.035447329 0.044852734 0.081921082 0.028754344 0.088352404
[22] 0.031105238 0.043023956 0.056128657 0.008268931 0.059556324 0.011996140 0.055913675
[29] 0.038489753 0.069742675 0.058810100 0.050482755 0.075441598 0.062385694 0.022242465
[36] 0.063442404
[[14]][[2]]$yf
[1] 0.12831642 0.05203472 0.07676249 0.05735523 0.05203472 0.11120614 0.07676249 0.12831642
[9] 0.10248331 0.07676249 0.07630820 0.07676249 0.02277750 0.08396360 0.02277750 0.02971421
[17] 0.03696854 0.04393834 0.08396360 0.02971421 0.08396360 0.02971421 0.04393834 0.05849609
[25] 0.01013254 0.05849609 0.01013254 0.05849609 0.03696854 0.06974268 0.05735523 0.05203472
[33] 0.07676249 0.05849609 0.02277750 0.06344240
[[14]][[3]]
[[15]]
[[15]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 -0.02456990 -0.0078054647
FRP_1_2 -0.06012271 -0.0035496882
FRP_1_3 -0.03971974 0.0009540191
FRP_2_1 0.03998716 -0.0309370731
FRP_2_2 0.03188282 -0.0042321271
FRP_2_3 0.01937631 -0.0483915539
FRP_3_1 -0.02026605 0.0127691874
FRP_3_2 0.02771215 0.0566577272
FRP_3_3 0.02571995 0.0245349733
$centroids
PCoA1 PCoA2
1 -0.04139507 -0.002919834
2 0.03182273 -0.029372792
3 0.01090157 0.030844533
attr(,"class")
[1] "ordiplot"
[[15]][[2]]
[[15]][[2]]$x
[1] 0.08627085 0.07467077 0.09069655 0.09513708 0.09352712 0.07587892 0.10805343 0.09550277
[9] 0.07349903 0.11643696 0.10814451 0.10779682 0.08859526 0.12135347 0.11213361 0.10300098
[17] 0.10276712 0.08966838 0.07844306 0.10174117 0.10139020 0.07714854 0.06936040 0.09424953
[25] 0.10131648 0.09631371 0.09041941 0.08726381 0.10165937 0.08276320 0.10290547 0.11187175
[33] 0.10304963 0.10068219 0.09694484 0.09950881
[[15]][[2]]$y
[1] 0.04834254 0.02161578 0.05058223 0.05466773 0.04786761 0.02162042 0.07044269 0.05873546
[9] 0.02714228 0.09572114 0.10289209 0.08044237 0.05554656 0.10162854 0.10509404 0.07119872
[17] 0.07626376 0.06205428 0.03039378 0.07982009 0.07812098 0.02202406 0.03157749 0.06187510
[25] 0.08873590 0.04801430 0.05239793 0.05800210 0.07212595 0.02743176 0.06730121 0.10770321
[33] 0.07494797 0.05043938 0.05148136 0.04694849
[[15]][[2]]$yf
[1] 0.04834254 0.02479601 0.05373942 0.05373942 0.05373942 0.02479601 0.07593996 0.05373942
[9] 0.02479601 0.10260780 0.10260780 0.07593996 0.05373942 0.10260780 0.10260780 0.07593996
[17] 0.07593996 0.05373942 0.02891277 0.07593996 0.07593996 0.02479601 0.02479601 0.05373942
[25] 0.07593996 0.05373942 0.05373942 0.05373942 0.07593996 0.02891277 0.07593996 0.10260780
[33] 0.07593996 0.05373942 0.05373942 0.05373942
[[15]][[3]]
[[16]]
[[16]][[1]]
$sites
PCoA1 PCoA2
FRP_1_2 -0.4565473 -0.0009434912
FRP_2_1 -0.4481572 -0.0033794703
FRP_1_1 0.3647707 -0.1605863750
FRP_1_3 -0.4735575 -0.0020271124
FRP_2_2 -0.4540831 0.0008995818
FRP_3_1 0.3437789 0.1997244792
FRP_3_3 0.3741651 -0.0859375311
FRP_2_3 0.3722042 0.0280109316
FRP_3_2 0.3774263 0.0242389874
$centroids
PCoA1 PCoA2
1 -0.4457850 -0.0043218452
2 -0.4284775 -0.0006543993
3 0.3774263 0.0242390033
attr(,"class")
[1] "ordiplot"
[[16]][[2]]
[[16]][[2]]$x
[1] 0.12959188 0.84032087 0.06865736 0.11057519 0.82838352 0.83890884 0.83388625 0.83815497
[9] 0.83269335 0.13069629 0.07872825 0.82198437 0.83153749 0.82598902 0.83126876 0.85680253
[17] 0.83781769 0.36220241 0.11457519 0.20839526 0.20070079 0.11483284 0.84493338 0.85537177
[25] 0.85074094 0.85566454 0.82528251 0.83667436 0.83090591 0.83559903 0.29374275 0.19503828
[33] 0.19595278 0.13939317 0.13921123 0.08413552
[[16]][[2]]$y
[1] 0.25447710 565.62302200 0.21031959 0.12091152 565.40820578 565.59495216
[7] 565.45730305 565.55112045 565.49797865 0.33685185 0.13742228 565.28299192
[13] 565.46977205 565.33218773 565.42599762 565.81035035 565.54528211 0.48528651
[19] 0.35015389 0.24738371 0.21519273 0.26508507 565.59546051 565.78222148
[25] 565.64460034 565.73841450 565.33039465 565.51715513 565.37953309 565.47334735
[31] 0.20567264 0.25619786 0.27277321 0.21511317 0.15261439 0.09574866
[[16]][[2]]$yf
[1] 0.2519560 565.6092413 0.1411005 0.1411005 565.3938694 565.5949522 565.4762097
[8] 565.5511205 565.4762097 0.2519560 0.1411005 565.2829919 565.4697721 565.3321877
[15] 565.4259976 565.8103504 565.5452821 0.4852865 0.2519560 0.2519560 0.2519560
[22] 0.2519560 565.6092413 565.7603180 565.6446003 565.7603180 565.3303947 565.5171551
[29] 565.3938694 565.4762097 0.2519560 0.2519560 0.2519560 0.2519560 0.2519560
[36] 0.1411005
[[16]][[3]]
[[17]]
[[17]][[1]]
$sites
PCoA1 PCoA2
FRP_1_1 0.01317558 0.057018703
FRP_1_2 -0.14263115 0.034215725
FRP_1_3 -0.03390554 0.033936430
FRP_2_1 -0.10294663 -0.078107663
FRP_2_2 -0.01872972 -0.013878459
FRP_2_3 0.06794507 -0.025960404
FRP_3_1 0.02757863 0.001359694
FRP_3_2 0.07424929 0.007446930
FRP_3_3 0.11526447 -0.016030957
$centroids
PCoA1 PCoA2
1 -0.04205007 0.038135972
2 -0.01872970 -0.013878539
3 0.07434876 0.003617549
attr(,"class")
[1] "ordiplot"
[[17]][[2]]
[[17]][[2]]$x
[1] 0.18840692 0.11562999 0.18314765 0.10093731 0.12583074 0.10582942 0.11015630 0.15834665
[9] 0.13306012 0.13981477 0.14184660 0.22532892 0.18971964 0.22203512 0.26560511 0.14742165
[17] 0.09537047 0.13504411 0.11900675 0.13569655 0.16460378 0.11721231 0.18754497 0.16595795
[25] 0.20236074 0.23481570 0.09758637 0.08891775 0.10698964 0.14377495 0.10401717 0.06297104
[33] 0.07524520 0.07969613 0.11864910 0.06970581
[[17]][[2]]$y
[1] 0.32196494 0.20006260 0.22088137 0.11168194 0.17236386 0.07804538 0.16834946 0.24901440
[9] 0.17278395 0.17503967 0.23290982 0.33689371 0.32122760 0.34622992 0.41847056 0.20807817
[17] 0.08866121 0.16447658 0.16737690 0.17425771 0.24627094 0.19461203 0.32480315 0.26204863
[25] 0.32887516 0.41598295 0.13021797 0.08832286 0.13476313 0.22140441 0.09448960 0.01224378
[33] 0.09118654 0.09033007 0.17300189 0.08792388
[[17]][[2]]$yf
[1] 0.32266523 0.17710835 0.24455384 0.10360872 0.17710835 0.10360872 0.16834946 0.24455384
[9] 0.17710835 0.17710835 0.22079747 0.34156182 0.32266523 0.34156182 0.41847056 0.22079747
[17] 0.08962517 0.17710835 0.17710835 0.17710835 0.24455384 0.17710835 0.32266523 0.24455384
[25] 0.32887516 0.41598295 0.10360872 0.08962517 0.13476313 0.22079747 0.10360872 0.01224378
[33] 0.08962517 0.08962517 0.17710835 0.08792388
[[17]][[3]]
[[18]]
[[18]][[1]]
$sites
PCoA1 PCoA2
FRP_3_1 0.105596144 -0.021325568
FRP_1_1 -0.066600410 0.027909600
FRP_1_2 -0.035287019 -0.020264373
FRP_1_3 -0.019748002 -0.062198954
FRP_2_1 -0.003049028 -0.058744369
FRP_2_2 -0.004816502 0.056526821
FRP_2_3 0.023839836 0.008949593
FRP_3_2 0.031377266 0.067192442
FRP_3_3 -0.031312285 0.001954807
$centroids
PCoA1 PCoA2
1 -0.03716566 -0.020070974
2 0.01448872 0.006329528
3 0.03059691 0.023254901
attr(,"class")
[1] "ordiplot"
[[18]][[2]]
[[18]][[2]]$x
[1] 0.18219357 0.14318786 0.13945648 0.13659006 0.14024335 0.10839739 0.13291422 0.14763386
[9] 0.07405135 0.11034382 0.12075680 0.08545951 0.11037669 0.11573331 0.08106146 0.06739269
[17] 0.08759362 0.08898974 0.08594184 0.12879086 0.05293174 0.05323006 0.12270565 0.10126061
[25] 0.14416067 0.09031536 0.13154407 0.09007812 0.13120021 0.10433042 0.08416310 0.06624057
[33] 0.08304585 0.07719591 0.07516047 0.11677145
[[18]][[2]]$y
[1] 0.292321175 0.226235208 0.214118034 0.166656620 0.221601343 0.141459807 0.167920077
[8] 0.232720252 0.086992115 0.164492218 0.179953640 0.090194696 0.151060055 0.176201841
[15] 0.078998826 0.081099750 0.093279843 0.098014528 0.090818034 0.161172184 0.008120363
[22] 0.047472319 0.171260695 0.119049074 0.212556176 0.087989802 0.161531264 0.087693041
[29] 0.183799799 0.101390953 0.092225149 0.086069432 0.095224136 0.096136261 0.095814125
[36] 0.162019852
[[18]][[2]]$yf
[1] 0.292321175 0.220130909 0.214118034 0.170327754 0.220130909 0.141459807 0.170327754
[8] 0.232720252 0.086992115 0.157776136 0.170327754 0.091929904 0.157776136 0.169110846
[15] 0.090316404 0.083584591 0.091929904 0.091929904 0.091929904 0.170327754 0.008120363
[22] 0.047472319 0.170327754 0.110220014 0.220130909 0.091929904 0.170327754 0.091929904
[29] 0.170327754 0.110220014 0.091929904 0.083584591 0.091929904 0.090316404 0.090316404
[36] 0.169110846
[[18]][[3]]
[[19]]
[[19]][[1]]
$sites
PCoA1 PCoA2
FRP_1_2 0.0444601405 -0.0216096941
FRP_3_3 -0.0453399997 -0.0289116660
FRP_3_2 0.0464638373 -0.0159208413
FRP_2_2 -0.0458488432 0.0053054021
FRP_2_3 0.0104043911 0.0252458669
FRP_3_1 0.0138771942 -0.0003034433
FRP_2_1 0.0003415477 0.0221493374
FRP_1_3 0.0172867403 0.0161506964
FRP_1_1 -0.0416450082 -0.0021056581
$centroids
PCoA1 PCoA2
1 0.014388335 0.007896744
2 -0.002599866 0.020936118
3 0.013764139 -0.003511919
attr(,"class")
[1] "ordiplot"
[[19]][[2]]
[[19]][[2]]$x
[1] 0.09085869 0.02337141 0.09596493 0.06028502 0.03889996 0.06529771 0.05066655 0.09034789
[9] 0.09476172 0.04362363 0.07917507 0.07132417 0.07045267 0.07934011 0.03140956 0.09718028
[17] 0.06027608 0.04098046 0.06266884 0.04832538 0.08982244 0.06648336 0.05948141 0.05625081
[25] 0.06875000 0.02535126 0.03899505 0.03009547 0.03077166 0.06273180 0.03463583 0.02995577
[33] 0.05810217 0.03097032 0.05215542 0.06427192
[[19]][[2]]$y
[1] 0.1586431318 0.0001806508 0.1583971202 0.1051713312 0.0572636238 0.1054668710
[7] 0.0744532133 0.1411175284 0.1586507719 0.0568496262 0.1428856761 0.1197218818
[13] 0.1127601933 0.1398781910 0.0408002278 0.1583405856 0.1050160004 0.0571559946
[19] 0.1053441744 0.0742976827 0.1410808403 0.1050082793 0.1056065084 0.0762998208
[25] 0.1135058135 0.0242331322 0.0568045398 0.0302394679 0.0307188213 0.1046347978
[31] 0.0489248604 0.0310279693 0.0923707704 0.0402449081 0.0744277209 0.1063791965
[[19]][[2]]$yf
[1] 0.1585079024 0.0001806508 0.1585079024 0.1051545625 0.0570184461 0.1056181156
[7] 0.0744404671 0.1412405589 0.1585079024 0.0570184461 0.1412405589 0.1197218818
[13] 0.1131330034 0.1412405589 0.0408002278 0.1585079024 0.1051545625 0.0570184461
[19] 0.1051545625 0.0742976827 0.1412405589 0.1056181156 0.1051545625 0.0762998208
[25] 0.1131330034 0.0242331322 0.0570184461 0.0306337186 0.0307188213 0.1051545625
[31] 0.0489248604 0.0306337186 0.0923707704 0.0402449081 0.0744404671 0.1056181156
[[19]][[3]]
Vouchered Reference dataframe
Here, I’m using a loc list that doesn’t include 16Sfish and crust2 because they have too few samples to include.
# cycle over the list of loci for the full reference pool sample replicates
# using the bray-curtis function to test for dissimilarity
# two of the loci were removed because they had too little data remaining after the sodm filter step
lapply(loc_list19, bray_nmds_complete, sodm_filtered_df = vrp_sodm_filtered_df, sample = "VRP")Run 0 stress 0
Run 1 stress 0
... Procrustes: rmse 0.2188576 max resid 0.4546289
Run 2 stress 0
... Procrustes: rmse 0.1629029 max resid 0.3723626
Run 3 stress 0
... Procrustes: rmse 0.2600044 max resid 0.5112368
Run 4 stress 0
... Procrustes: rmse 0.1920451 max resid 0.3739882
Run 5 stress 0
... Procrustes: rmse 0.1419563 max resid 0.319324
Run 6 stress 0
... Procrustes: rmse 0.1375993 max resid 0.2651579
Run 7 stress 0
... Procrustes: rmse 0.164848 max resid 0.3344819
Run 8 stress 0
... Procrustes: rmse 0.162067 max resid 0.2551065
Run 9 stress 0
... Procrustes: rmse 0.1838458 max resid 0.4614907
Run 10 stress 0
... Procrustes: rmse 0.1531954 max resid 0.3104926
Run 11 stress 0
... Procrustes: rmse 0.09379692 max resid 0.1764086
Run 12 stress 0
... Procrustes: rmse 0.2336251 max resid 0.5324595
Run 13 stress 0
... Procrustes: rmse 0.2495365 max resid 0.455896
Run 14 stress 0
... Procrustes: rmse 0.2658785 max resid 0.4391367
Run 15 stress 0
... Procrustes: rmse 0.2080438 max resid 0.4265525
Run 16 stress 0
... Procrustes: rmse 0.1905128 max resid 0.3659933
Run 17 stress 0
... Procrustes: rmse 0.2073191 max resid 0.4117981
Run 18 stress 0
... Procrustes: rmse 0.198308 max resid 0.4213292
Run 19 stress 0
... Procrustes: rmse 0.2051783 max resid 0.4216974
Run 20 stress 0
... Procrustes: rmse 0.1355869 max resid 0.3115212
Run 21 stress 0
... Procrustes: rmse 0.195923 max resid 0.3282201
Run 22 stress 0
... Procrustes: rmse 0.1724445 max resid 0.3703548
Run 23 stress 0
... Procrustes: rmse 0.1269243 max resid 0.2568244
Run 24 stress 0
... Procrustes: rmse 0.2256089 max resid 0.4080003
Run 25 stress 0
... Procrustes: rmse 0.08165474 max resid 0.1588491
Run 26 stress 0
... Procrustes: rmse 0.1797413 max resid 0.3708846
Run 27 stress 0
... Procrustes: rmse 0.0983635 max resid 0.1810968
Run 28 stress 0
... Procrustes: rmse 0.1301974 max resid 0.2868027
Run 29 stress 0
... Procrustes: rmse 0.1944609 max resid 0.3642681
Run 30 stress 0
... Procrustes: rmse 0.2436758 max resid 0.4675065
Run 31 stress 0
... Procrustes: rmse 0.1974465 max resid 0.5133868
Run 32 stress 0
... Procrustes: rmse 0.2363754 max resid 0.3267545
Run 33 stress 0
... Procrustes: rmse 0.2146592 max resid 0.3925539
Run 34 stress 0
... Procrustes: rmse 0.2075408 max resid 0.4523453
Run 35 stress 0
... Procrustes: rmse 0.1653941 max resid 0.2666775
Run 36 stress 0
... Procrustes: rmse 0.1317495 max resid 0.2416324
Run 37 stress 0
... Procrustes: rmse 0.1682703 max resid 0.3440028
Run 38 stress 0
... Procrustes: rmse 0.08457228 max resid 0.1493885
Run 39 stress 1.30749e-06
... Procrustes: rmse 0.2471044 max resid 0.6337704
Run 40 stress 0
... Procrustes: rmse 0.1091712 max resid 0.1842388
Run 41 stress 0
... Procrustes: rmse 0.1468511 max resid 0.3256452
Run 42 stress 0
... Procrustes: rmse 0.2280831 max resid 0.3475688
Run 43 stress 0
... Procrustes: rmse 0.170635 max resid 0.3911123
Run 44 stress 0
... Procrustes: rmse 0.2733204 max resid 0.5613543
Run 45 stress 0
... Procrustes: rmse 0.1332195 max resid 0.2680989
Run 46 stress 0
... Procrustes: rmse 0.1364323 max resid 0.2322551
Run 47 stress 0
... Procrustes: rmse 0.1750729 max resid 0.3704281
Run 48 stress 0
... Procrustes: rmse 0.2258418 max resid 0.4570286
Run 49 stress 0
... Procrustes: rmse 0.2048435 max resid 0.4489906
Run 50 stress 0
... Procrustes: rmse 0.2463745 max resid 0.4592324
*** No convergence -- monoMDS stopping criteria:
50: stress < smin
Run 0 stress 0.1259422
Run 1 stress 0.1103133
... New best solution
... Procrustes: rmse 0.2637142 max resid 0.5224047
Run 2 stress 0.1416419
Run 3 stress 0.1259422
Run 4 stress 0.1036948
... New best solution
... Procrustes: rmse 0.1513322 max resid 0.2323675
Run 5 stress 0.1292795
Run 6 stress 0.1036937
... New best solution
... Procrustes: rmse 0.001168286 max resid 0.002549205
... Similar to previous best
Run 7 stress 0.1206489
Run 8 stress 0.1036958
... Procrustes: rmse 0.001443218 max resid 0.00314999
... Similar to previous best
Run 9 stress 0.103697
... Procrustes: rmse 0.001631093 max resid 0.003551549
... Similar to previous best
Run 10 stress 0.1036941
... Procrustes: rmse 0.0002481308 max resid 0.0004712785
... Similar to previous best
Run 11 stress 0.1206521
Run 12 stress 0.1036955
... Procrustes: rmse 0.00117882 max resid 0.002568815
... Similar to previous best
Run 13 stress 0.1259422
Run 14 stress 0.1259424
Run 15 stress 0.1259422
Run 16 stress 0.2803009
Run 17 stress 0.1259422
Run 18 stress 0.1206492
Run 19 stress 0.1259422
Run 20 stress 0.3209239
*** Solution reached
Run 0 stress 0.03964791
Run 1 stress 0.04315421
Run 2 stress 0.03964791
... Procrustes: rmse 1.980161e-05 max resid 2.832945e-05
... Similar to previous best
Run 3 stress 0.03964791
... Procrustes: rmse 2.805544e-05 max resid 4.056985e-05
... Similar to previous best
Run 4 stress 0.03964791
... New best solution
... Procrustes: rmse 5.244541e-06 max resid 7.488455e-06
... Similar to previous best
Run 5 stress 0.1112105
Run 6 stress 0.111211
Run 7 stress 0.03964791
... New best solution
... Procrustes: rmse 1.366879e-06 max resid 2.249539e-06
... Similar to previous best
Run 8 stress 0.03964791
... Procrustes: rmse 4.194253e-06 max resid 7.180948e-06
... Similar to previous best
Run 9 stress 0.1112105
Run 10 stress 0.04315421
Run 11 stress 0.1112111
Run 12 stress 0.1112098
Run 13 stress 0.03964791
... Procrustes: rmse 2.337427e-05 max resid 3.664673e-05
... Similar to previous best
Run 14 stress 0.03964791
... Procrustes: rmse 3.228929e-06 max resid 4.435384e-06
... Similar to previous best
Run 15 stress 0.1084866
Run 16 stress 0.03964791
... Procrustes: rmse 1.035472e-05 max resid 2.173901e-05
... Similar to previous best
Run 17 stress 0.1112101
Run 18 stress 0.03964791
... Procrustes: rmse 4.697961e-06 max resid 6.970804e-06
... Similar to previous best
Run 19 stress 0.03964791
... New best solution
... Procrustes: rmse 4.849198e-06 max resid 7.792353e-06
... Similar to previous best
Run 20 stress 0.1112105
*** Solution reached
some squared distances are negative and changed to zero
Run 0 stress 8.667746e-05
Run 1 stress 9.536068e-05
... Procrustes: rmse 0.108884 max resid 0.2666471
Run 2 stress 9.91464e-05
... Procrustes: rmse 0.09868257 max resid 0.2408404
Run 3 stress 9.801766e-05
... Procrustes: rmse 0.1054047 max resid 0.258108
Run 4 stress 9.225491e-05
... Procrustes: rmse 0.1115615 max resid 0.2732391
Run 5 stress 9.936466e-05
... Procrustes: rmse 0.04523827 max resid 0.1068417
Run 6 stress 8.641996e-05
... New best solution
... Procrustes: rmse 0.110557 max resid 0.2707826
Run 7 stress 9.755808e-05
... Procrustes: rmse 0.01668631 max resid 0.03539528
Run 8 stress 9.276799e-05
... Procrustes: rmse 0.1605222 max resid 0.3273854
Run 9 stress 7.891082e-05
... New best solution
... Procrustes: rmse 0.1750057 max resid 0.4082376
Run 10 stress 9.935081e-05
... Procrustes: rmse 0.1484668 max resid 0.3602935
Run 11 stress 9.934168e-05
... Procrustes: rmse 0.05826092 max resid 0.1413558
Run 12 stress 9.014264e-05
... Procrustes: rmse 0.1354521 max resid 0.3280625
Run 13 stress 9.892543e-05
... Procrustes: rmse 0.1723239 max resid 0.4220054
Run 14 stress 9.738839e-05
... Procrustes: rmse 0.1680317 max resid 0.4113084
Run 15 stress 9.951748e-05
... Procrustes: rmse 0.08788538 max resid 0.2067694
Run 16 stress 9.932458e-05
... Procrustes: rmse 0.1746533 max resid 0.4277728
Run 17 stress 9.645076e-05
... Procrustes: rmse 0.08944167 max resid 0.2181974
Run 18 stress 9.814548e-05
... Procrustes: rmse 0.1557908 max resid 0.3798346
Run 19 stress 9.695131e-05
... Procrustes: rmse 0.09101006 max resid 0.2221463
Run 20 stress 9.709462e-05
... Procrustes: rmse 0.09020712 max resid 0.2180217
Run 21 stress 9.776125e-05
... Procrustes: rmse 0.02232116 max resid 0.05260948
Run 22 stress 9.727769e-05
... Procrustes: rmse 0.08804021 max resid 0.2124437
Run 23 stress 9.707723e-05
... Procrustes: rmse 0.1515489 max resid 0.3686039
Run 24 stress 9.681252e-05
... Procrustes: rmse 0.08551088 max resid 0.2086257
Run 25 stress 9.738063e-05
... Procrustes: rmse 0.1697696 max resid 0.4156666
Run 26 stress 9.246671e-05
... Procrustes: rmse 0.08090248 max resid 0.1917372
Run 27 stress 9.571305e-05
... Procrustes: rmse 0.09685932 max resid 0.2345325
Run 28 stress 9.619452e-05
... Procrustes: rmse 0.09309699 max resid 0.215885
Run 29 stress 9.88892e-05
... Procrustes: rmse 0.0740892 max resid 0.1781816
Run 30 stress 0.2967445
Run 31 stress 9.941774e-05
... Procrustes: rmse 0.03570365 max resid 0.08464137
Run 32 stress 8.397398e-05
... Procrustes: rmse 0.05195618 max resid 0.1239748
Run 33 stress 9.993281e-05
... Procrustes: rmse 0.172526 max resid 0.4225068
Run 34 stress 9.789951e-05
... Procrustes: rmse 0.1715659 max resid 0.4201453
Run 35 stress 9.174099e-05
... Procrustes: rmse 0.1475248 max resid 0.3577374
Run 36 stress 9.513745e-05
... Procrustes: rmse 0.1427368 max resid 0.3445499
Run 37 stress 9.740113e-05
... Procrustes: rmse 0.07944222 max resid 0.1936961
Run 38 stress 9.819195e-05
... Procrustes: rmse 0.0656421 max resid 0.1574147
Run 39 stress 8.678904e-05
... Procrustes: rmse 0.107735 max resid 0.261588
Run 40 stress 8.69852e-05
... Procrustes: rmse 0.06050472 max resid 0.1448305
Run 41 stress 9.151744e-05
... Procrustes: rmse 0.02544703 max resid 0.06006112
Run 42 stress 9.421919e-05
... Procrustes: rmse 0.09068855 max resid 0.2165869
Run 43 stress 0.2249798
Run 44 stress 9.784529e-05
... Procrustes: rmse 0.02778264 max resid 0.06596256
Run 45 stress 9.706405e-05
... Procrustes: rmse 0.1667612 max resid 0.4081171
Run 46 stress 9.786297e-05
... Procrustes: rmse 0.01495359 max resid 0.03512935
Run 47 stress 7.723104e-05
... New best solution
... Procrustes: rmse 0.08219489 max resid 0.2004547
Run 48 stress 9.615278e-05
... Procrustes: rmse 0.07837847 max resid 0.1855386
Run 49 stress 9.73395e-05
... Procrustes: rmse 0.07521555 max resid 0.1624063
Run 50 stress 7.831879e-05
... Procrustes: rmse 0.004114803 max resid 0.01001169
*** No convergence -- monoMDS stopping criteria:
48: stress < smin
2: stress ratio > sratmaxstress is (nearly) zero: you may have insufficient data
some squared distances are negative and changed to zero
Run 0 stress 0.004057148
Run 1 stress 0.0003132056
... New best solution
... Procrustes: rmse 0.09563141 max resid 0.173432
Run 2 stress 0.003820962
Run 3 stress 6.86615e-05
... New best solution
... Procrustes: rmse 0.0116565 max resid 0.02065372
Run 4 stress 0.002475264
Run 5 stress 9.796909e-05
... Procrustes: rmse 0.0001525007 max resid 0.0003597428
... Similar to previous best
Run 6 stress 0.0007867326
Run 7 stress 0.001464736
Run 8 stress 0.002370016
Run 9 stress 0.002321086
Run 10 stress 0.002824514
Run 11 stress 9.958852e-05
... Procrustes: rmse 0.002435118 max resid 0.00436641
... Similar to previous best
Run 12 stress 0.004279178
Run 13 stress 0.004615126
Run 14 stress 0.00401314
Run 15 stress 0.001003602
Run 16 stress 0.0019895
Run 17 stress 0.003512334
Run 18 stress 0.003696047
Run 19 stress 0.004449227
Run 20 stress 0.003443399
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 9.067646e-05
Run 1 stress 9.110231e-05
... Procrustes: rmse 0.0001779459 max resid 0.0002989909
... Similar to previous best
Run 2 stress 9.627185e-05
... Procrustes: rmse 0.0001066613 max resid 0.0002234183
... Similar to previous best
Run 3 stress 9.188034e-05
... Procrustes: rmse 0.000144028 max resid 0.0002822105
... Similar to previous best
Run 4 stress 9.42809e-05
... Procrustes: rmse 0.0001069846 max resid 0.0002163624
... Similar to previous best
Run 5 stress 9.234793e-05
... Procrustes: rmse 9.078537e-05 max resid 0.0002245651
... Similar to previous best
Run 6 stress 9.650997e-05
... Procrustes: rmse 0.0001000753 max resid 0.0002303269
... Similar to previous best
Run 7 stress 9.720027e-05
... Procrustes: rmse 0.0001236748 max resid 0.0002430165
... Similar to previous best
Run 8 stress 9.961986e-05
... Procrustes: rmse 5.621712e-05 max resid 9.223319e-05
... Similar to previous best
Run 9 stress 9.771733e-05
... Procrustes: rmse 0.0001735538 max resid 0.0003894828
... Similar to previous best
Run 10 stress 9.169103e-05
... Procrustes: rmse 8.635932e-05 max resid 0.0001791235
... Similar to previous best
Run 11 stress 9.675115e-05
... Procrustes: rmse 9.405712e-05 max resid 0.0002193741
... Similar to previous best
Run 12 stress 9.699617e-05
... Procrustes: rmse 0.0002161336 max resid 0.0005675132
... Similar to previous best
Run 13 stress 9.972287e-05
... Procrustes: rmse 0.0001013219 max resid 0.0002289973
... Similar to previous best
Run 14 stress 9.548317e-05
... Procrustes: rmse 8.897567e-05 max resid 0.0002134352
... Similar to previous best
Run 15 stress 9.556614e-05
... Procrustes: rmse 9.665983e-05 max resid 0.0002294433
... Similar to previous best
Run 16 stress 8.517561e-05
... New best solution
... Procrustes: rmse 0.0001441305 max resid 0.0002731599
... Similar to previous best
Run 17 stress 9.660906e-05
... Procrustes: rmse 0.0001702649 max resid 0.0003421176
... Similar to previous best
Run 18 stress 9.228205e-05
... Procrustes: rmse 0.0002270476 max resid 0.0003242311
... Similar to previous best
Run 19 stress 7.838671e-05
... New best solution
... Procrustes: rmse 0.0002053979 max resid 0.0004514357
... Similar to previous best
Run 20 stress 9.675485e-05
... Procrustes: rmse 0.0002246021 max resid 0.0005204136
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.06478732
Run 1 stress 0.06478732
... New best solution
... Procrustes: rmse 1.991994e-05 max resid 4.444007e-05
... Similar to previous best
Run 2 stress 0.06478732
... Procrustes: rmse 4.59711e-06 max resid 6.783002e-06
... Similar to previous best
Run 3 stress 0.08468917
Run 4 stress 0.218923
Run 5 stress 0.2189312
Run 6 stress 0.3017338
Run 7 stress 0.08384273
Run 8 stress 0.301734
Run 9 stress 0.1238453
Run 10 stress 0.06478732
... Procrustes: rmse 1.827482e-05 max resid 4.011759e-05
... Similar to previous best
Run 11 stress 0.2468083
Run 12 stress 0.1309035
Run 13 stress 0.2178622
Run 14 stress 0.1222038
Run 15 stress 0.06478732
... New best solution
... Procrustes: rmse 1.403047e-05 max resid 2.984715e-05
... Similar to previous best
Run 16 stress 0.08384279
Run 17 stress 0.06478732
... New best solution
... Procrustes: rmse 7.778366e-06 max resid 1.613612e-05
... Similar to previous best
Run 18 stress 0.06478732
... Procrustes: rmse 1.097479e-05 max resid 2.355169e-05
... Similar to previous best
Run 19 stress 0.08384276
Run 20 stress 0.2274463
*** Solution reached
Run 0 stress 0.0001737962
Run 1 stress 0.1931245
Run 2 stress 0.1922478
Run 3 stress 0.0002433636
... Procrustes: rmse 0.0006440908 max resid 0.001544935
... Similar to previous best
Run 4 stress 0.0001469373
... New best solution
... Procrustes: rmse 0.0006505572 max resid 0.001500907
... Similar to previous best
Run 5 stress 0.0001690772
... Procrustes: rmse 0.000678394 max resid 0.001572084
... Similar to previous best
Run 6 stress 0.0006338134
... Procrustes: rmse 0.002760331 max resid 0.00385252
... Similar to previous best
Run 7 stress 9.905228e-05
... New best solution
... Procrustes: rmse 0.000606058 max resid 0.0009650649
... Similar to previous best
Run 8 stress 0.0001002189
... Procrustes: rmse 0.0003396107 max resid 0.0005805789
... Similar to previous best
Run 9 stress 0.000603401
Run 10 stress 0.0002985038
... Procrustes: rmse 0.001452848 max resid 0.00213755
... Similar to previous best
Run 11 stress 0.192936
Run 12 stress 0.0002158335
... Procrustes: rmse 0.0008466959 max resid 0.00127293
... Similar to previous best
Run 13 stress 0.0002426834
... Procrustes: rmse 0.0009669963 max resid 0.001426538
... Similar to previous best
Run 14 stress 0.0001083423
... Procrustes: rmse 0.0004467831 max resid 0.0007365517
... Similar to previous best
Run 15 stress 0.0004160257
... Procrustes: rmse 0.001704275 max resid 0.00244946
... Similar to previous best
Run 16 stress 9.73418e-05
... New best solution
... Procrustes: rmse 3.854303e-05 max resid 6.233984e-05
... Similar to previous best
Run 17 stress 0.0002492047
... Procrustes: rmse 0.001032235 max resid 0.001547507
... Similar to previous best
Run 18 stress 9.71039e-05
... New best solution
... Procrustes: rmse 0.0002951521 max resid 0.0005020085
... Similar to previous best
Run 19 stress 0.0002124182
... Procrustes: rmse 0.0007835771 max resid 0.001452022
... Similar to previous best
Run 20 stress 0.001143199
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.
Set of permutations < 'minperm'. Generating entire set.
the matrix is either rank-deficient or indefiniteRun 0 stress 7.005617e-05
Run 1 stress 0
... New best solution
... Procrustes: rmse 0.1107594 max resid 0.1620621
Run 2 stress 0
... Procrustes: rmse 0.1796376 max resid 0.296941
Run 3 stress 0
... Procrustes: rmse 0.1603009 max resid 0.2613614
Run 4 stress 0
... Procrustes: rmse 0.1370571 max resid 0.2268672
Run 5 stress 0.2601588
Run 6 stress 5.601201e-05
... Procrustes: rmse 0.1501562 max resid 0.25019
Run 7 stress 0
... Procrustes: rmse 0.175267 max resid 0.3406301
Run 8 stress 7.882424e-05
... Procrustes: rmse 0.1178408 max resid 0.2233217
Run 9 stress 0
... Procrustes: rmse 0.1208735 max resid 0.2365515
Run 10 stress 0
... Procrustes: rmse 0.1594542 max resid 0.3395309
Run 11 stress 0
... Procrustes: rmse 0.1683528 max resid 0.2825622
Run 12 stress 0
... Procrustes: rmse 0.1359023 max resid 0.2316057
Run 13 stress 0
... Procrustes: rmse 0.1272357 max resid 0.2125166
Run 14 stress 0.2913768
Run 15 stress 0
... Procrustes: rmse 0.1594966 max resid 0.348734
Run 16 stress 0
... Procrustes: rmse 0.1480589 max resid 0.3209884
Run 17 stress 0
... Procrustes: rmse 0.1396237 max resid 0.2583611
Run 18 stress 0
... Procrustes: rmse 0.1802635 max resid 0.3671116
Run 19 stress 0
... Procrustes: rmse 0.1088744 max resid 0.1581856
Run 20 stress 0
... Procrustes: rmse 0.140263 max resid 0.1975136
Run 21 stress 0
... Procrustes: rmse 0.1679227 max resid 0.2902029
Run 22 stress 0
... Procrustes: rmse 0.1080097 max resid 0.1884412
Run 23 stress 4.096519e-05
... Procrustes: rmse 0.1460704 max resid 0.3262926
Run 24 stress 0
... Procrustes: rmse 0.1768473 max resid 0.3074839
Run 25 stress 0.260151
Run 26 stress 0
... Procrustes: rmse 0.1433172 max resid 0.2840299
Run 27 stress 0
... Procrustes: rmse 0.1310975 max resid 0.2911339
Run 28 stress 0
... Procrustes: rmse 0.1909139 max resid 0.3431758
Run 29 stress 0
... Procrustes: rmse 0.1359499 max resid 0.2487249
Run 30 stress 0.260161
Run 31 stress 0
... Procrustes: rmse 0.1477025 max resid 0.2357143
Run 32 stress 0
... Procrustes: rmse 0.1334867 max resid 0.2737578
Run 33 stress 0
... Procrustes: rmse 0.186326 max resid 0.2922697
Run 34 stress 0
... Procrustes: rmse 0.1267352 max resid 0.2841199
Run 35 stress 8.700007e-05
... Procrustes: rmse 0.1811012 max resid 0.3637296
Run 36 stress 0
... Procrustes: rmse 0.1555964 max resid 0.331628
Run 37 stress 0
... Procrustes: rmse 0.1448856 max resid 0.231232
Run 38 stress 4.74369e-05
... Procrustes: rmse 0.1453227 max resid 0.2714403
Run 39 stress 0
... Procrustes: rmse 0.1162664 max resid 0.2549876
Run 40 stress 0
... Procrustes: rmse 0.07351639 max resid 0.09561597
Run 41 stress 0
... Procrustes: rmse 0.1520385 max resid 0.2624539
Run 42 stress 0
... Procrustes: rmse 0.1503577 max resid 0.2311533
Run 43 stress 8.33597e-05
... Procrustes: rmse 0.1054097 max resid 0.1683178
Run 44 stress 0
... Procrustes: rmse 0.05465973 max resid 0.07291582
Run 45 stress 3.410929e-05
... Procrustes: rmse 0.1521829 max resid 0.2687246
Run 46 stress 0
... Procrustes: rmse 0.1337994 max resid 0.2301535
Run 47 stress 0
... Procrustes: rmse 0.123918 max resid 0.2469821
Run 48 stress 5.73814e-05
... Procrustes: rmse 0.1243357 max resid 0.2026426
Run 49 stress 0
... Procrustes: rmse 0.1422029 max resid 0.2488459
Run 50 stress 0
... Procrustes: rmse 0.155961 max resid 0.3128638
*** No convergence -- monoMDS stopping criteria:
46: stress < smin
4: stress ratio > sratmaxstress is (nearly) zero: you may have insufficient data
some squared distances are negative and changed to zero
Run 0 stress 8.721965e-05
Run 1 stress 9.495963e-05
... Procrustes: rmse 0.0752607 max resid 0.1856571
Run 2 stress 9.709662e-05
... Procrustes: rmse 0.1298015 max resid 0.2482023
Run 3 stress 0.0002908939
... Procrustes: rmse 0.1163453 max resid 0.261744
Run 4 stress 9.737233e-05
... Procrustes: rmse 0.1839662 max resid 0.4454657
Run 5 stress 9.915997e-05
... Procrustes: rmse 0.1683944 max resid 0.4424191
Run 6 stress 8.933734e-05
... Procrustes: rmse 0.1717334 max resid 0.4424444
Run 7 stress 9.063125e-05
... Procrustes: rmse 0.1290613 max resid 0.2966678
Run 8 stress 9.652917e-05
... Procrustes: rmse 0.122026 max resid 0.2911875
Run 9 stress 8.721457e-05
... New best solution
... Procrustes: rmse 0.09269199 max resid 0.2044008
Run 10 stress 0.0002030336
... Procrustes: rmse 0.1650057 max resid 0.4308755
Run 11 stress 8.954966e-05
... Procrustes: rmse 0.1891889 max resid 0.4601668
Run 12 stress 0.0004168325
... Procrustes: rmse 0.1882785 max resid 0.4711072
Run 13 stress 9.899608e-05
... Procrustes: rmse 0.1746658 max resid 0.4501998
Run 14 stress 9.779146e-05
... Procrustes: rmse 0.1945713 max resid 0.4570796
Run 15 stress 2.295362e-07
... New best solution
... Procrustes: rmse 0.2096509 max resid 0.5417649
Run 16 stress 8.43171e-05
... Procrustes: rmse 0.1464804 max resid 0.3160826
Run 17 stress 8.269528e-05
... Procrustes: rmse 0.08111843 max resid 0.1694908
Run 18 stress 9.611796e-05
... Procrustes: rmse 0.06059572 max resid 0.1441053
Run 19 stress 0.000583308
Run 20 stress 7.926188e-05
... Procrustes: rmse 0.09739839 max resid 0.2342326
Run 21 stress 7.08114e-05
... Procrustes: rmse 0.05497349 max resid 0.1434307
Run 22 stress 9.60515e-05
... Procrustes: rmse 0.2081029 max resid 0.3967444
Run 23 stress 9.985001e-05
... Procrustes: rmse 0.1822 max resid 0.3268183
Run 24 stress 9.523672e-05
... Procrustes: rmse 0.1277837 max resid 0.2870385
Run 25 stress 9.880334e-05
... Procrustes: rmse 0.1691981 max resid 0.3453624
Run 26 stress 9.797208e-05
... Procrustes: rmse 0.1943246 max resid 0.3932757
Run 27 stress 7.991742e-05
... Procrustes: rmse 0.1897103 max resid 0.3489437
Run 28 stress 9.827434e-05
... Procrustes: rmse 0.1601055 max resid 0.3465772
Run 29 stress 9.902841e-05
... Procrustes: rmse 0.1579787 max resid 0.315932
Run 30 stress 9.411416e-05
... Procrustes: rmse 0.1804202 max resid 0.3870789
Run 31 stress 9.302819e-05
... Procrustes: rmse 0.08922465 max resid 0.1891959
Run 32 stress 8.65736e-05
... Procrustes: rmse 0.1894873 max resid 0.3524702
Run 33 stress 9.718201e-05
... Procrustes: rmse 0.1549785 max resid 0.3107519
Run 34 stress 5.462037e-05
... Procrustes: rmse 0.04579491 max resid 0.1272207
Run 35 stress 9.204787e-05
... Procrustes: rmse 0.164304 max resid 0.3518353
Run 36 stress 9.954443e-05
... Procrustes: rmse 0.1778288 max resid 0.4212087
Run 37 stress 9.533226e-05
... Procrustes: rmse 0.1582482 max resid 0.3399884
Run 38 stress 0.0003033731
... Procrustes: rmse 0.1296228 max resid 0.2192902
Run 39 stress 9.385977e-05
... Procrustes: rmse 0.1774193 max resid 0.3570189
Run 40 stress 0.0003136235
... Procrustes: rmse 0.105874 max resid 0.220973
Run 41 stress 7.00375e-05
... Procrustes: rmse 0.08064397 max resid 0.2193751
Run 42 stress 9.224654e-10
... New best solution
... Procrustes: rmse 0.02366539 max resid 0.06630255
Run 43 stress 0.0001876882
... Procrustes: rmse 0.1343535 max resid 0.3226501
Run 44 stress 8.217977e-05
... Procrustes: rmse 0.01139482 max resid 0.03152576
Run 45 stress 0.0006526166
Run 46 stress 9.822717e-05
... Procrustes: rmse 0.1698526 max resid 0.3530765
Run 47 stress 9.487946e-05
... Procrustes: rmse 0.09787196 max resid 0.2184816
Run 48 stress 9.952979e-05
... Procrustes: rmse 0.1930848 max resid 0.3729796
Run 49 stress 9.782336e-05
... Procrustes: rmse 0.1757682 max resid 0.3737311
Run 50 stress 0.0005531539
*** No convergence -- monoMDS stopping criteria:
9: no. of iterations >= maxit
41: stress < sminstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.001330486
Run 1 stress 0.0102618
Run 2 stress 0.01068341
Run 3 stress 0.0101777
Run 4 stress 0.01011898
Run 5 stress 0.01074989
Run 6 stress 0.009865147
Run 7 stress 0.001455574
... Procrustes: rmse 0.002008137 max resid 0.003504469
... Similar to previous best
Run 8 stress 0.01026857
Run 9 stress 0.002942602
Run 10 stress 0.001258874
... New best solution
... Procrustes: rmse 0.001137115 max resid 0.001987802
... Similar to previous best
Run 11 stress 0.01036499
Run 12 stress 0.01006273
Run 13 stress 0.001096652
... New best solution
... Procrustes: rmse 0.002649618 max resid 0.004636221
... Similar to previous best
Run 14 stress 0.01033084
Run 15 stress 0.01038906
Run 16 stress 0.0006190737
... New best solution
... Procrustes: rmse 0.02161587 max resid 0.03826
Run 17 stress 0.003199082
Run 18 stress 0.002976297
Run 19 stress 0.002914593
Run 20 stress 0.1776138
Run 21 stress 0.01054381
Run 22 stress 0.0011561
Run 23 stress 0.009984864
Run 24 stress 0.1776123
Run 25 stress 0.0008842209
... Procrustes: rmse 0.002038128 max resid 0.003713254
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.003910892
Run 1 stress 0.01767479
Run 2 stress 0.006896669
Run 3 stress 0.004224086
... Procrustes: rmse 0.008537337 max resid 0.02009377
Run 4 stress 0.01742178
Run 5 stress 0.00784041
Run 6 stress 0.006803662
Run 7 stress 0.01746948
Run 8 stress 0.2380299
Run 9 stress 0.0174127
Run 10 stress 0.1579801
Run 11 stress 0.00489736
Run 12 stress 0.1946672
Run 13 stress 0.0180764
Run 14 stress 0.004218569
... Procrustes: rmse 0.008802041 max resid 0.0206495
Run 15 stress 0.004998118
Run 16 stress 0.2005064
Run 17 stress 0.004134582
... Procrustes: rmse 0.007469317 max resid 0.01764092
Run 18 stress 0.01741947
Run 19 stress 0.004016489
... Procrustes: rmse 0.005170946 max resid 0.01217771
Run 20 stress 0.006803634
Run 21 stress 0.01745716
Run 22 stress 0.004073168
... Procrustes: rmse 0.006764288 max resid 0.01597491
Run 23 stress 0.01814757
Run 24 stress 0.1579716
Run 25 stress 0.003981175
... Procrustes: rmse 0.003910477 max resid 0.009209736
... Similar to previous best
*** Solution reached
Run 0 stress 0.1006496
Run 1 stress 0.1031526
Run 2 stress 0.1031526
Run 3 stress 0.1951269
Run 4 stress 0.1597999
Run 5 stress 0.1640799
Run 6 stress 0.1083668
Run 7 stress 0.1083617
Run 8 stress 0.1641053
Run 9 stress 0.3100932
Run 10 stress 0.1035243
Run 11 stress 0.2103553
Run 12 stress 0.1031522
Run 13 stress 0.1083657
Run 14 stress 0.1951269
Run 15 stress 0.2374606
Run 16 stress 0.1035243
Run 17 stress 0.2098428
Run 18 stress 0.1629503
Run 19 stress 0.1035244
Run 20 stress 0.1035245
Run 21 stress 0.1035246
Run 22 stress 0.2268951
Run 23 stress 0.1951269
Run 24 stress 0.1598002
Run 25 stress 0.1035245
Run 26 stress 0.1031521
Run 27 stress 0.1640513
Run 28 stress 0.1630402
Run 29 stress 0.1640898
Run 30 stress 0.161274
Run 31 stress 0.1035243
Run 32 stress 0.103152
Run 33 stress 0.1630402
Run 34 stress 0.1031522
Run 35 stress 0.1006497
... Procrustes: rmse 0.0001298946 max resid 0.0002462838
... Similar to previous best
*** Solution reached
Run 0 stress 0.003726447
Run 1 stress 0.0009149695
... New best solution
... Procrustes: rmse 0.02844682 max resid 0.04292799
Run 2 stress 0.3209238
Run 3 stress 0.001159242
... Procrustes: rmse 0.001153499 max resid 0.00166699
... Similar to previous best
Run 4 stress 0.0002495404
... New best solution
... Procrustes: rmse 0.003605675 max resid 0.005143764
... Similar to previous best
Run 5 stress 0.0001886906
... New best solution
... Procrustes: rmse 0.0002580389 max resid 0.000353918
... Similar to previous best
Run 6 stress 0.002553226
Run 7 stress 0.0004351715
... Procrustes: rmse 0.001598463 max resid 0.00248278
... Similar to previous best
Run 8 stress 0.0009720799
Run 9 stress 0.008038564
Run 10 stress 0.001897718
Run 11 stress 0.008382712
Run 12 stress 0.005082917
Run 13 stress 0.001027933
Run 14 stress 0.003232986
Run 15 stress 0.006398985
Run 16 stress 0.0037748
Run 17 stress 0.005736606
Run 18 stress 9.904321e-05
... New best solution
... Procrustes: rmse 0.0005232668 max resid 0.0009571667
... Similar to previous best
Run 19 stress 0.3209238
Run 20 stress 0.0009093694
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.009886766
Run 1 stress 0.009886895
... Procrustes: rmse 4.4742e-05 max resid 6.820768e-05
... Similar to previous best
Run 2 stress 0.009886792
... Procrustes: rmse 2.660776e-05 max resid 4.872767e-05
... Similar to previous best
Run 3 stress 0.009887335
... Procrustes: rmse 0.0007348911 max resid 0.001012578
... Similar to previous best
Run 4 stress 0.01181363
Run 5 stress 0.01181326
Run 6 stress 0.01181387
Run 7 stress 0.009887669
... Procrustes: rmse 0.0002639188 max resid 0.0003577166
... Similar to previous best
Run 8 stress 0.003137305
... New best solution
... Procrustes: rmse 0.1486293 max resid 0.2778697
Run 9 stress 0.01181365
Run 10 stress 0.01181345
Run 11 stress 0.01181296
Run 12 stress 0.009887095
Run 13 stress 0.01181365
Run 14 stress 0.0118136
Run 15 stress 0.009887865
Run 16 stress 0.001644788
... New best solution
... Procrustes: rmse 0.00570225 max resid 0.007827323
Run 17 stress 0.009887305
Run 18 stress 0.009887326
Run 19 stress 0.009895394
Run 20 stress 0.01181307
Run 21 stress 0.3209238
Run 22 stress 0.01181312
Run 23 stress 0.00988735
Run 24 stress 0.01181334
Run 25 stress 0.002179876
Run 26 stress 0.01181389
Run 27 stress 0.009886813
Run 28 stress 0.01181368
Run 29 stress 0.01181331
Run 30 stress 0.01181327
Run 31 stress 0.2958243
Run 32 stress 0.0118134
Run 33 stress 0.01181344
Run 34 stress 0.01181327
Run 35 stress 0.009887246
Run 36 stress 0.01181372
Run 37 stress 0.01181351
Run 38 stress 0.01181346
Run 39 stress 0.01181296
Run 40 stress 0.009887811
Run 41 stress 0.2834628
Run 42 stress 0.01181342
Run 43 stress 0.01181365
Run 44 stress 0.01181335
Run 45 stress 0.009888144
Run 46 stress 0.009887007
Run 47 stress 0.01181356
Run 48 stress 0.009887006
Run 49 stress 0.01181306
Run 50 stress 0.01181297
*** No convergence -- monoMDS stopping criteria:
5: no. of iterations >= maxit
45: stress ratio > sratmax
Run 0 stress 0.0008020932
Run 1 stress 9.750691e-05
... New best solution
... Procrustes: rmse 0.005116532 max resid 0.01010663
Run 2 stress 8.201927e-05
... New best solution
... Procrustes: rmse 4.230489e-05 max resid 8.577289e-05
... Similar to previous best
Run 3 stress 0.003095419
Run 4 stress 9.747516e-05
... Procrustes: rmse 0.0001994593 max resid 0.0003831759
... Similar to previous best
Run 5 stress 9.62684e-05
... Procrustes: rmse 0.0001480487 max resid 0.0002623351
... Similar to previous best
Run 6 stress 0.001049042
Run 7 stress 9.805017e-05
... Procrustes: rmse 0.0002148108 max resid 0.0003794942
... Similar to previous best
Run 8 stress 9.988109e-05
... Procrustes: rmse 0.0004962097 max resid 0.0007997795
... Similar to previous best
Run 9 stress 9.654156e-05
... Procrustes: rmse 3.960846e-05 max resid 8.15097e-05
... Similar to previous best
Run 10 stress 0.001782582
Run 11 stress 0.0004128235
... Procrustes: rmse 0.002564904 max resid 0.005030343
... Similar to previous best
Run 12 stress 0.001249741
Run 13 stress 0.001739429
Run 14 stress 0.00223367
Run 15 stress 0.0003976754
... Procrustes: rmse 0.002468066 max resid 0.004829322
... Similar to previous best
Run 16 stress 8.279852e-05
... Procrustes: rmse 0.000216879 max resid 0.0003501307
... Similar to previous best
Run 17 stress 0.001141836
Run 18 stress 9.424054e-05
... Procrustes: rmse 0.0001940248 max resid 0.0003631561
... Similar to previous best
Run 19 stress 0.001593474
Run 20 stress 0.0005702038
... Procrustes: rmse 0.003608715 max resid 0.007123898
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.02472531
Run 1 stress 0.02617798
Run 2 stress 0.05285309
Run 3 stress 0.05285051
Run 4 stress 0.03732498
Run 5 stress 0.04150701
Run 6 stress 0.02472567
... Procrustes: rmse 0.000229733 max resid 0.0004080513
... Similar to previous best
Run 7 stress 0.05285139
Run 8 stress 0.02617855
Run 9 stress 0.05285179
Run 10 stress 0.04022859
Run 11 stress 0.04150743
Run 12 stress 0.301653
Run 13 stress 0.05285061
Run 14 stress 0.02617792
Run 15 stress 0.03732486
Run 16 stress 0.02617779
Run 17 stress 0.03732444
Run 18 stress 0.04022848
Run 19 stress 0.02472566
... Procrustes: rmse 0.0005635939 max resid 0.00102827
... Similar to previous best
Run 20 stress 0.02617833
*** Solution reached
Run 0 stress 0.004654572
Run 1 stress 0.004561244
... New best solution
... Procrustes: rmse 0.002390258 max resid 0.005049396
... Similar to previous best
Run 2 stress 0.005741514
Run 3 stress 0.0008310096
... New best solution
... Procrustes: rmse 0.1096484 max resid 0.2378611
Run 4 stress 9.855991e-05
... New best solution
... Procrustes: rmse 0.03548357 max resid 0.07626931
Run 5 stress 9.905774e-05
... Procrustes: rmse 0.0002814818 max resid 0.0005079338
... Similar to previous best
Run 6 stress 0.0001503091
... Procrustes: rmse 0.006685041 max resid 0.01460539
Run 7 stress 0.001230588
Run 8 stress 0.3208797
Run 9 stress 9.694505e-05
... New best solution
... Procrustes: rmse 0.0002783379 max resid 0.0004954861
... Similar to previous best
Run 10 stress 0.002387915
Run 11 stress 9.590866e-05
... New best solution
... Procrustes: rmse 2.062539e-05 max resid 3.436255e-05
... Similar to previous best
Run 12 stress 0.002054987
Run 13 stress 9.733518e-05
... Procrustes: rmse 0.0002204859 max resid 0.0004065847
... Similar to previous best
Run 14 stress 0.002523767
Run 15 stress 0.003432957
Run 16 stress 0.004301808
Run 17 stress 0.001559285
Run 18 stress 0.002766787
Run 19 stress 0.001771348
Run 20 stress 9.859705e-05
... Procrustes: rmse 2.374201e-05 max resid 4.710894e-05
... Similar to previous best
*** Solution reachedstress is (nearly) zero: you may have insufficient data
Run 0 stress 0.01498623
Run 1 stress 0.01498611
... New best solution
... Procrustes: rmse 0.0001193423 max resid 0.0002216734
... Similar to previous best
Run 2 stress 0.01498609
... New best solution
... Procrustes: rmse 1.773182e-05 max resid 2.390395e-05
... Similar to previous best
Run 3 stress 0.3209238
Run 4 stress 0.01498617
... Procrustes: rmse 8.827194e-05 max resid 0.0001580609
... Similar to previous best
Run 5 stress 0.2583166
Run 6 stress 0.01498609
... Procrustes: rmse 2.014819e-05 max resid 3.335632e-05
... Similar to previous best
Run 7 stress 0.301736
Run 8 stress 0.01498651
... Procrustes: rmse 0.0001554673 max resid 0.0002823505
... Similar to previous best
Run 9 stress 0.01498619
... Procrustes: rmse 0.0001052337 max resid 0.0001877758
... Similar to previous best
Run 10 stress 0.1433568
Run 11 stress 0.0149864
... Procrustes: rmse 0.0001855524 max resid 0.0003442151
... Similar to previous best
Run 12 stress 0.01498637
... Procrustes: rmse 0.0001795198 max resid 0.000332003
... Similar to previous best
Run 13 stress 0.01498626
... Procrustes: rmse 0.0001342418 max resid 0.0002461645
... Similar to previous best
Run 14 stress 0.1287859
Run 15 stress 0.01498609
... Procrustes: rmse 4.749228e-06 max resid 6.683217e-06
... Similar to previous best
Run 16 stress 0.01498634
... Procrustes: rmse 0.0001563341 max resid 0.0002864291
... Similar to previous best
Run 17 stress 0.01498622
... Procrustes: rmse 0.0001114253 max resid 0.0002008367
... Similar to previous best
Run 18 stress 0.01498611
... Procrustes: rmse 3.89444e-05 max resid 6.233891e-05
... Similar to previous best
Run 19 stress 0.01498615
... Procrustes: rmse 7.650915e-05 max resid 0.0001353694
... Similar to previous best
Run 20 stress 0.1287859
*** Solution reached
[[1]]
[[1]][[1]]
$sites
PCoA1 PCoA2
VRP_1_2 0.5862686842 5.000000e-01
VRP_3_2 -0.1047214513 -1.570092e-15
VRP_1_3 -0.2763765091 1.030373e-15
VRP_2_1 -0.2642310057 1.167756e-15
VRP_2_2 0.0254217337 -4.035628e-15
VRP_2_3 -0.2757490867 1.246261e-15
VRP_3_1 -0.2763765091 1.246261e-15
VRP_3_3 -0.0005045401 -3.576867e-15
VRP_1_1 0.5862686842 -5.000000e-01
$centroids
PCoA1 PCoA2
1 0.2987202 3.338430e-15
2 -0.2449256 7.621935e-16
3 -0.1392895 -1.083007e-15
attr(,"class")
[1] "ordiplot"
[[1]][[2]]
[[1]][[2]]$x
[1] 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000 1.00000000
[9] 0.60000000 0.60000000 0.73076923 0.60000000 0.60000000 0.70879121 1.00000000 0.21250000
[17] 0.73076923 0.06722689 0.00000000 0.70879121 1.00000000 0.73076923 0.21250000 0.21250000
[25] 0.70879121 1.00000000 0.73076923 0.73076923 0.73076923 1.00000000 0.06722689 0.70879121
[33] 1.00000000 0.70879121 1.00000000 1.00000000
[[1]][[2]]$y
[1] 4.238532e+00 4.439044e+00 4.443675e+00 3.204349e+00 4.439497e+00 4.439044e+00
[7] 3.830185e+00 4.570788e+00 2.359216e-01 2.413218e-01 1.323542e+00 2.364503e-01
[13] 2.359216e-01 4.959681e-01 4.238532e+00 5.400175e-03 1.559464e+00 5.286974e-04
[19] 2.773856e-16 7.318897e-01 4.439044e+00 1.564864e+00 4.871477e-03 5.400175e-03
[25] 7.372899e-01 4.443675e+00 1.559993e+00 1.559464e+00 8.275744e-01 3.204349e+00
[31] 5.286974e-04 7.324184e-01 4.439497e+00 7.318897e-01 4.439044e+00 3.830185e+00
[[1]][[2]]$yf
[1] 4.238532e+00 4.439044e+00 4.443675e+00 3.204349e+00 4.439497e+00 4.439044e+00
[7] 3.830185e+00 4.570788e+00 2.359216e-01 2.413218e-01 1.323542e+00 2.364503e-01
[13] 2.359216e-01 4.959681e-01 4.238532e+00 5.400175e-03 1.559464e+00 5.286974e-04
[19] 2.773856e-16 7.318897e-01 4.439044e+00 1.564864e+00 4.871477e-03 5.400175e-03
[25] 7.372899e-01 4.443675e+00 1.559993e+00 1.559464e+00 8.275744e-01 3.204349e+00
[31] 5.286974e-04 7.324184e-01 4.439497e+00 7.318897e-01 4.439044e+00 3.830185e+00
[[1]][[3]]
[[2]]
[[2]][[1]]
$sites
PCoA1 PCoA2
VRP_2_2 0.06223194 -0.03218835
VRP_3_2 -0.12143039 -0.08428135
VRP_1_1 -0.03924415 0.41973318
VRP_1_2 -0.30722804 -0.03446703
VRP_1_3 0.09108614 -0.18428576
VRP_2_1 0.18101590 0.01197154
VRP_2_3 0.25283684 0.01347461
VRP_3_3 0.06108066 -0.04542514
VRP_3_1 -0.18034891 -0.06453169
$centroids
PCoA1 PCoA2
1 -0.11745679 0.034163892
2 0.18962177 0.004250358
3 -0.09201998 -0.065915552
attr(,"class")
[1] "ordiplot"
[[2]][[2]]
[[2]][[2]]$x
[1] 0.5032051 0.6149790 0.5334101 0.5153319 0.5238848 0.5045845 0.4845350 0.5407875 0.5551639
[10] 0.3723634 0.3907011 0.4637906 0.4803642 0.3952268 0.3411745 0.5531478 0.6345116 0.5139555
[19] 0.5580446 0.5428889 0.5501391 0.4873470 0.5354037 0.5966125 0.4939780 0.2518451 0.3496873
[28] 0.4210040 0.3861088 0.4290666 0.3222381 0.3551889 0.4182878 0.4359211 0.4909468 0.3807462
[[2]][[2]]$y
[1] 0.4600318 1.1179237 0.6920834 0.3168000 0.6058212 0.4570879 0.4929546 0.6270031 0.8068699
[10] 0.2514792 0.2203721 0.4396437 0.5146830 0.2496545 0.2067686 0.8310892 0.8118237 0.5255981
[19] 0.7589168 0.6332716 0.6100067 0.4701074 0.6152138 0.7468399 0.4461997 0.2694334 0.3299042
[28] 0.3118611 0.1792103 0.3245754 0.2500015 0.1904821 0.3530236 0.3123646 0.5246327 0.2126948
[[2]][[2]]$yf
[1] 0.4675661 0.9648737 0.6355157 0.4675661 0.6058212 0.4675661 0.4675661 0.6355157 0.7859290
[10] 0.2344829 0.2344829 0.4396437 0.4675661 0.2496545 0.2344829 0.7859290 0.9648737 0.4675661
[19] 0.7859290 0.6355157 0.6355157 0.4675661 0.6355157 0.7859290 0.4675661 0.2344829 0.2344829
[28] 0.3254562 0.2344829 0.3254562 0.2344829 0.2344829 0.3254562 0.3254562 0.4675661 0.2344829
[[2]][[3]]
[[3]]
[[3]][[1]]
$sites
PCoA1 PCoA2
VRP_3_1 0.029052046 -0.0047338085
VRP_1_1 -0.055733432 0.0205083265
VRP_1_2 -0.027371046 -0.0315120710
VRP_1_3 0.005723366 0.0009047258
VRP_2_1 0.008891801 -0.0052788598
VRP_2_2 0.003247065 0.0057336522
VRP_2_3 0.016370296 0.0472680986
VRP_3_2 0.011433932 -0.0186441995
VRP_3_3 0.008385972 -0.0142458642
$centroids
PCoA1 PCoA2
1 -0.024920004 -0.006837472
2 0.006780712 0.008980220
3 0.013529282 -0.013588374
attr(,"class")
[1] "ordiplot"
[[3]][[2]]
[[3]][[2]]$x
[1] 0.09118262 0.06679724 0.04947584 0.05116147 0.04731814 0.05931034 0.04486558 0.03817052
[9] 0.06459339 0.07212132 0.07754841 0.06646357 0.07921552 0.08064126 0.07488133 0.06023513
[17] 0.05759675 0.05838419 0.09088092 0.05358339 0.05174796 0.04378628 0.04179200 0.05981422
[25] 0.04285236 0.04162236 0.03329178 0.06307684 0.04244733 0.04202763 0.05350693 0.04113854
[33] 0.03983053 0.07057321 0.06692789 0.02945824
[[3]][[2]]$y
[1] 0.0912955449 0.0681278354 0.0106406370 0.0160599952 0.0179234013 0.0623067436
[7] 0.0137044791 0.0129804829 0.0579051267 0.0806564366 0.0759031964 0.0735214797
[13] 0.0780084706 0.0826461566 0.0826011211 0.0601541573 0.0538897075 0.0539181511
[19] 0.0975457191 0.0545952429 0.0552217927 0.0063052412 0.0074122219 0.0574332770
[25] 0.0100198644 0.0090984181 0.0031148412 0.0594722408 0.0085996225 0.0080320632
[31] 0.0567901432 0.0117141342 0.0111408031 0.0671349079 0.0662823246 0.0009434977
[[3]][[2]]$yf
[1] 0.0944206320 0.0687666369 0.0142820192 0.0160599952 0.0142820192 0.0594543091
[7] 0.0137044791 0.0094780946 0.0594543091 0.0792923062 0.0792923062 0.0687666369
[13] 0.0792923062 0.0826461566 0.0792923062 0.0594543091 0.0548830075 0.0548830075
[19] 0.0944206320 0.0548830075 0.0548830075 0.0094780946 0.0094780946 0.0594543091
[25] 0.0094780946 0.0094780946 0.0031148412 0.0594543091 0.0094780946 0.0094780946
[31] 0.0548830075 0.0094780946 0.0094780946 0.0687666369 0.0687666369 0.0009434977
[[3]][[3]]
[[4]]
[[4]][[1]]
$sites
PCoA1 PCoA2
VRP_2_3 0.3449351 0.115830925
VRP_3_1 0.3522500 -0.224617031
VRP_2_2 -0.1740941 -0.018454748
VRP_1_1 -0.1582541 -0.020485535
VRP_1_2 -0.1780778 0.012370314
VRP_1_3 0.3828341 0.105291041
VRP_2_1 -0.1784519 0.027414389
VRP_3_2 -0.1967549 -0.005775657
VRP_3_3 -0.1943863 0.008426301
$centroids
PCoA1 PCoA2
1 -0.1398127 -0.004960608
2 -0.1461517 0.015793066
3 -0.1863440 -0.003347964
attr(,"class")
[1] "ordiplot"
[[4]][[2]]
[[4]][[2]]$x
[1] 0.34351650 0.55883229 0.54612438 0.53434534 0.17224712 0.53252109 0.55498082 0.54919820
[9] 0.56712642 0.55352480 0.58222433 0.34965670 0.59102600 0.59323452 0.59564535 0.05415415
[17] 0.07258085 0.56305667 0.06008295 0.08218148 0.07318827 0.07803641 0.54948760 0.08227694
[25] 0.10994541 0.09560619 0.58225731 0.10210716 0.06351451 0.05162704 0.58513639 0.60672609
[33] 0.60048775 0.12069414 0.11217268 0.03539800
[[4]][[2]]$y
[1] 0.5859078343 1.0367568538 1.0366357009 1.0367336909 0.4858224942 1.0367496365
[7] 1.0369402657 1.0368135824 1.0369230413 1.0367997780 1.0367984550 1.0357483844
[13] 1.0370382712 1.0369392367 1.0368247813 0.0001274544 0.0001953007 1.0370496793
[19] 0.0002238863 0.0003136825 0.0002751228 0.0001828117 1.0369598551 0.0002869282
[25] 0.0003727344 0.0002904552 1.0371173882 0.0004179934 0.0002152607 0.0001097713
[31] 1.0369413256 1.0373288631 1.0372227994 0.0005148538 0.0004971158 0.0001275395
[[4]][[2]]$yf
[1] 0.5859078343 1.0368641881 1.0367063428 1.0367063428 0.4858224942 1.0367063428
[7] 1.0368641881 1.0368135824 1.0369237252 1.0368641881 1.0369237252 1.0357483844
[13] 1.0369722006 1.0369722006 1.0369722006 0.0001274544 0.0002114826 1.0369237252
[19] 0.0002114826 0.0002970219 0.0002289672 0.0002289672 1.0368641881 0.0002970219
[25] 0.0003953639 0.0002970219 1.0369722006 0.0003953639 0.0002114826 0.0001186554
[31] 1.0369722006 1.0373288631 1.0372227994 0.0005148538 0.0004971158 0.0001186554
[[4]][[3]]
[[5]]
[[5]][[1]]
$sites
PCoA1 PCoA2
VRP_3_1 -0.078753712 -0.011303242
VRP_1_2 -0.158482581 0.159849075
VRP_3_2 -0.054120998 0.005917372
VRP_1_3 -0.095069288 -0.056606724
VRP_2_1 -0.003542966 -0.117214228
VRP_2_2 -0.088084421 -0.012443024
VRP_2_3 0.056884088 -0.070588143
VRP_3_3 -0.134244891 0.050724267
VRP_1_1 0.555414768 0.051664647
$centroids
PCoA1 PCoA2
1 -0.05641014 0.015386273
2 -0.00498768 -0.097158767
3 -0.06603741 0.008252513
attr(,"class")
[1] "ordiplot"
[[5]][[2]]
[[5]][[2]]$x
[1] 0.19953601 0.08615449 0.06644644 0.13742331 0.03890593 0.21793879 0.15793554 0.63870983
[9] 0.19600840 0.24012520 0.31184462 0.21583370 0.33374020 0.14258375 0.72366111 0.10472028
[17] 0.14772727 0.11722488 0.15247588 0.10656912 0.61350068 0.12316093 0.05752362 0.20974035
[25] 0.13696550 0.65936008 0.16297588 0.11404617 0.24599799 0.58575638 0.24837058 0.16429344
[33] 0.64974470 0.21232877 0.52599433 0.69525659
[[5]][[2]]$y
[1] 2.029188e-04 8.472393e-05 2.604755e-05 2.499066e-04 2.882273e-05 2.906740e-04
[7] 1.638216e-04 1.128394e+00 2.411203e-04 2.080866e-04 2.590841e-04 2.119123e-04
[13] 3.069065e-04 3.213432e-04 1.128586e+00 5.910499e-05 1.899850e-04 5.593277e-05
[19] 2.233910e-04 8.522818e-05 1.128345e+00 2.274649e-04 4.164064e-06 2.669564e-04
[25] 1.404602e-04 1.128382e+00 2.270434e-04 4.858523e-05 2.003562e-04 1.128405e+00
[31] 2.660566e-04 1.366376e-04 1.128378e+00 2.167423e-04 1.128378e+00 1.128267e+00
[[5]][[2]]$yf
[1] 2.220196e-04 6.671502e-05 2.604755e-05 2.160183e-04 1.649340e-05 2.330389e-04
[7] 2.160183e-04 1.128364e+00 2.220196e-04 2.330389e-04 2.625704e-04 2.318703e-04
[13] 3.069065e-04 2.160183e-04 1.128586e+00 6.671502e-05 2.160183e-04 6.671502e-05
[19] 2.160183e-04 6.671502e-05 1.128364e+00 1.839625e-04 1.649340e-05 2.318703e-04
[25] 1.839625e-04 1.128364e+00 2.160183e-04 6.671502e-05 2.330389e-04 1.128364e+00
[31] 2.625704e-04 2.160183e-04 1.128364e+00 2.318703e-04 1.128364e+00 1.128364e+00
[[5]][[3]]
[[6]]
[[6]][[1]]
$sites
PCoA1 PCoA2
VRP_2_1 -0.010418287 0.018869202
VRP_1_3 -0.014215969 -0.012706185
VRP_2_2 -0.007894429 0.039597847
VRP_3_1 -0.006908415 -0.017288518
VRP_3_2 -0.042628112 0.004762452
VRP_1_2 -0.003856702 -0.023998680
VRP_2_3 0.078133558 0.012344215
VRP_3_3 -0.004183521 0.023927699
VRP_1_1 0.011971878 -0.045508032
$centroids
PCoA1 PCoA2
1 -0.003903216 -0.025013644
2 0.004654079 0.026372346
3 -0.016373164 0.004755486
attr(,"class")
[1] "ordiplot"
[[6]][[2]]
[[6]][[2]]$x
[1] 0.05946089 0.05248627 0.06793824 0.06535628 0.06661538 0.09864890 0.04643045 0.08063908
[9] 0.06945883 0.07357559 0.05299429 0.05609351 0.10118141 0.07390286 0.06955294 0.07968234
[17] 0.07220035 0.07874282 0.09956196 0.04938108 0.09413019 0.07123348 0.05844612 0.10263915
[25] 0.06289894 0.07333181 0.06784824 0.12209804 0.06699983 0.09463152 0.09707820 0.07432277
[33] 0.07127660 0.09495626 0.10217575 0.07900144
[[6]][[2]]$y
[1] 1.452369e-05 1.130464e-06 1.507015e-05 1.515380e-05 1.516122e-05 7.179031e-02
[7] 5.167531e-07 1.191644e-05 1.565154e-05 9.997450e-06 7.077562e-06 5.647854e-06
[13] 7.179050e-02 1.503238e-05 1.931375e-05 1.600515e-05 1.612818e-05 1.624150e-05
[19] 7.179037e-02 6.427542e-07 1.198406e-05 1.666483e-05 4.634939e-06 7.178089e-02
[25] 1.540911e-05 1.254797e-05 1.264065e-05 7.179748e-02 1.564826e-05 2.359336e-05
[31] 7.178486e-02 1.560133e-05 1.604279e-05 7.179021e-02 7.177840e-02 1.180528e-05
[[6]][[2]]$yf
[1] 1.452369e-05 1.130464e-06 1.470079e-05 1.470079e-05 1.470079e-05 7.178651e-02
[7] 5.167531e-07 1.470079e-05 1.470079e-05 1.470079e-05 5.786785e-06 5.786785e-06
[13] 7.178651e-02 1.470079e-05 1.470079e-05 1.470079e-05 1.470079e-05 1.470079e-05
[19] 7.178651e-02 6.427542e-07 1.470079e-05 1.470079e-05 5.786785e-06 7.178651e-02
[25] 1.470079e-05 1.470079e-05 1.470079e-05 7.179748e-02 1.470079e-05 2.359336e-05
[31] 7.178651e-02 1.470079e-05 1.470079e-05 7.178651e-02 7.178651e-02 1.470079e-05
[[6]][[3]]
[[7]]
[[7]][[1]]
$sites
PCoA1 PCoA2
VRP_1_2 0.025489376 -0.01695810
VRP_1_1 -0.029416857 -0.02347329
VRP_1_3 -0.067611854 -0.01830372
VRP_2_1 -0.007780106 -0.01865890
VRP_2_2 0.044163884 -0.01532530
VRP_2_3 0.035061663 -0.02407526
VRP_3_1 0.059413293 0.04044509
VRP_3_2 -0.049521632 0.04468230
VRP_3_3 -0.009797767 0.03166717
$centroids
PCoA1 PCoA2
1 -0.027164947 -0.02196136
2 0.026039435 -0.01860575
3 -0.007639575 0.03549524
attr(,"class")
[1] "ordiplot"
[[7]][[2]]
[[7]][[2]]$x
[1] 0.06589096 0.10429946 0.05421110 0.04161802 0.06753291 0.07491501 0.09923365 0.07649869
[9] 0.06554872 0.06414838 0.08978431 0.09123432 0.11421035 0.08082159 0.07632782 0.08053750
[17] 0.11937459 0.10512173 0.14165945 0.06706653 0.09009609 0.06548999 0.08301046 0.10237682
[25] 0.08598786 0.06315610 0.07213898 0.06965285 0.11375728 0.08843089 0.07692891 0.12170592
[33] 0.08731839 0.10846902 0.08241560 0.06164845
[[7]][[2]]$y
[1] 0.06607395 0.11868761 0.03508632 0.04979257 0.05342501 0.09972320 0.12283601 0.08777399
[9] 0.05950724 0.05618866 0.11547818 0.11141611 0.15868892 0.09398029 0.10049140 0.09463370
[17] 0.16445725 0.16874180 0.19608604 0.06480085 0.10980959 0.07095367 0.08772640 0.10416420
[25] 0.08836906 0.05677084 0.04546062 0.05847038 0.15472595 0.10114573 0.10203778 0.17602239
[33] 0.13413304 0.16670043 0.10175328 0.06577275
[[7]][[2]]$yf
[1] 0.05981310 0.11868761 0.04243945 0.04243945 0.05981310 0.09516546 0.11414041 0.09516546
[9] 0.05981310 0.05957742 0.11414041 0.11414041 0.16221428 0.09516546 0.09516546 0.09516546
[17] 0.16445725 0.16221428 0.19608604 0.05981310 0.11414041 0.05981310 0.09516546 0.11414041
[25] 0.09516546 0.05957742 0.05981310 0.05981310 0.16221428 0.11414041 0.09516546 0.17602239
[33] 0.11414041 0.16221428 0.09516546 0.05957742
[[7]][[3]]
[[8]]
[[8]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 -0.047020392 0.029430994
VRP_1_2 -0.035494717 -0.005177926
VRP_1_3 -0.038359554 0.003211699
VRP_2_1 -0.004869189 -0.024400240
VRP_2_2 -0.022008899 -0.011857746
VRP_2_3 -0.017321111 -0.005350773
VRP_3_1 0.049753469 -0.006809008
VRP_3_2 0.057954958 -0.021043581
VRP_3_3 0.057365436 0.041996581
$centroids
PCoA1 PCoA2
1 -0.03969643 0.0073636423
2 -0.01564581 -0.0128541931
3 0.05457603 0.0001890153
attr(,"class")
[1] "ordiplot"
[[8]][[2]]
[[8]][[2]]$x
[1] 0.07040735 0.07174566 0.08572843 0.07456677 0.07389112 0.11406713 0.12141064 0.11917415
[9] 0.06146231 0.08145671 0.05425631 0.06591610 0.10233776 0.10419012 0.11415045 0.07625631
[17] 0.05887041 0.06813572 0.10073352 0.11403012 0.11321237 0.05987092 0.05940354 0.08634579
[25] 0.08797748 0.09887814 0.05060967 0.09315227 0.09296135 0.10005260 0.08692778 0.09712586
[33] 0.09761141 0.06080515 0.07559474 0.07829820
[[8]][[2]]$y
[1] 4.145593e-05 7.040389e-05 1.193093e-04 8.106025e-05 8.269316e-05 7.368306e-02
[7] 7.369150e-02 7.369674e-02 3.095571e-05 7.988099e-05 4.358615e-05 4.714703e-05
[13] 7.367141e-02 7.367986e-02 7.368514e-02 6.423059e-05 4.017982e-05 4.647528e-05
[19] 7.367735e-02 7.368580e-02 7.369111e-02 3.870566e-05 3.908984e-05 7.362178e-02
[25] 7.363025e-02 7.363558e-02 6.557929e-06 7.363730e-02 7.364575e-02 7.365105e-02
[31] 7.363122e-02 7.363968e-02 7.364498e-02 2.442445e-05 9.073252e-05 6.698293e-05
[[8]][[2]]$yf
[1] 4.502608e-05 7.040389e-05 1.193093e-04 7.713989e-05 7.713989e-05 7.368628e-02
[7] 7.369412e-02 7.369412e-02 3.615694e-05 7.988099e-05 3.615694e-05 4.502608e-05
[13] 7.367438e-02 7.367986e-02 7.368628e-02 7.713989e-05 3.615694e-05 4.502608e-05
[19] 7.367438e-02 7.368628e-02 7.368628e-02 3.615694e-05 3.615694e-05 7.362178e-02
[25] 7.363074e-02 7.364066e-02 6.557929e-06 7.364066e-02 7.364066e-02 7.365105e-02
[31] 7.363074e-02 7.364066e-02 7.364066e-02 3.615694e-05 7.713989e-05 7.713989e-05
[[8]][[3]]
[[9]]
[[9]][[1]]
$sites
PCoA1 PCoA2
VRP_1_3 0.2218044 -0.005636428
VRP_2_1 -0.1277190 -0.167128143
VRP_2_2 0.2650836 -0.008374067
VRP_2_3 0.4096688 0.044302500
VRP_3_1 0.4092775 0.044653939
VRP_1_1 -0.5890577 0.046091100
VRP_1_2 -0.5890577 0.046091100
$centroids
PCoA1 PCoA2
1 -0.5890577 0.046091100
2 0.2650836 -0.008374074
3 0.4092775 0.044653939
attr(,"class")
[1] "ordiplot"
[[9]][[2]]
[[9]][[2]]$x
[1] 0.39561404 0.16206897 0.21666667 0.22592593 0.81666667 0.81666667 0.44101633 0.57894737
[9] 0.57894737 0.50877193 0.50877193 0.20689655 0.20689655 0.86206897 0.86206897 0.08217593
[17] 1.00000000 1.00000000 1.00000000 1.00000000 0.00000000
[[9]][[2]]$y
[1] 0.777116473 0.074343806 0.667166619 0.707642400 1.600323156 1.592374797 0.792847432
[8] 0.993447677 1.013069259 0.845786215 0.838813127 0.594957546 0.635635590 1.626693592
[15] 1.618985263 0.041226483 1.802740750 1.797335456 1.815115482 1.809884182 0.009604366
[[9]][[2]]$yf
[1] 0.777116473 0.074343806 0.667166619 0.707642400 1.600323156 1.592374797 0.792847432
[8] 0.993447677 1.013069259 0.845786215 0.838813127 0.594957546 0.635635590 1.626693592
[15] 1.618985263 0.041226483 1.802740750 1.797335456 1.815115482 1.809884182 0.009604366
[[9]][[3]]
[[10]]
[[10]][[1]]
$sites
PCoA1 PCoA2
VRP_2_2 0.003667869 0.011624612
VRP_3_1 -0.008585016 -0.002926648
VRP_3_3 -0.011798764 -0.005512777
VRP_1_1 0.033132381 -0.018166581
VRP_1_2 0.004739255 0.013885028
VRP_1_3 -0.011407492 -0.005143968
VRP_2_1 -0.011138131 -0.005464495
VRP_2_3 0.012923465 0.017121659
VRP_3_2 -0.011533567 -0.005416830
$centroids
PCoA1 PCoA2
1 0.0047402616 -0.0006787609
2 0.0007645708 0.0068569847
3 -0.0117987452 -0.0055127640
attr(,"class")
[1] "ordiplot"
[[10]][[2]]
[[10]][[2]]$x
[1] 0.0324616199 0.0326211357 0.0467528872 0.0338651905 0.0327477432 0.0324616199
[7] 0.0380935505 0.0325450335 0.0152673200 0.0466790462 0.0338651905 0.0189673106
[13] 0.0186073464 0.0380197095 0.0187646009 0.0469124030 0.0338651905 0.0085071263
[19] 0.0056323400 0.0382530663 0.0056323400 0.0471984043 0.0470390105 0.0464597233
[25] 0.0461208522 0.0468363008 0.0338651905 0.0338651905 0.0385390676 0.0338651905
[31] 0.0085071263 0.0383796738 0.0085071263 0.0378003866 0.0003765775 0.0381769641
[[10]][[2]]$y
[1] 7.550814e-11 6.614260e-11 4.311659e-02 2.465911e-04 6.603371e-11 9.913559e-11
[7] 1.420358e-03 6.008232e-11 9.604706e-12 4.311659e-02 2.465910e-04 1.313181e-11
[13] 2.367856e-11 1.420358e-03 2.285702e-11 4.311659e-02 2.465910e-04 1.049766e-11
[19] 3.300769e-11 1.420358e-03 1.867982e-11 4.336111e-02 4.311659e-02 4.311659e-02
[25] 4.170208e-02 4.311659e-02 2.465910e-04 2.465910e-04 1.661903e-03 2.465910e-04
[31] 3.516561e-11 1.420358e-03 9.726478e-12 1.420358e-03 4.420091e-11 1.420358e-03
[[10]][[2]]$yf
[1] 7.338047e-11 7.338047e-11 4.311659e-02 2.465911e-04 7.338047e-11 7.338047e-11
[7] 1.420358e-03 7.338047e-11 2.205503e-11 4.311659e-02 2.465910e-04 2.205503e-11
[13] 2.205503e-11 1.420358e-03 2.205503e-11 4.311659e-02 2.465910e-04 2.205503e-11
[19] 2.205503e-11 1.420358e-03 2.205503e-11 4.336111e-02 4.311659e-02 4.311659e-02
[25] 4.170208e-02 4.311659e-02 2.465910e-04 2.465910e-04 1.661903e-03 2.465910e-04
[31] 2.205503e-11 1.420358e-03 2.205503e-11 1.420358e-03 2.205503e-11 1.420358e-03
[[10]][[3]]
[[11]]
[[11]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 -0.078296780 -0.028806964
VRP_1_2 -0.167802267 0.045825683
VRP_1_3 -0.011252591 -0.007414339
VRP_2_1 0.055271485 0.015156543
VRP_2_2 -0.004217692 -0.027974662
VRP_2_3 0.110587643 0.052597951
VRP_3_1 0.026231806 -0.034657264
VRP_3_2 0.008795153 -0.007345337
VRP_3_3 0.060683244 -0.007381612
$centroids
PCoA1 PCoA2
1 -0.07867127 -0.008148539
2 0.05512076 0.014506719
3 0.02764335 -0.016480153
attr(,"class")
[1] "ordiplot"
[[11]][[2]]
[[11]][[2]]$x
[1] 0.14185636 0.11597255 0.15821364 0.11022280 0.21218861 0.14465832 0.13301447 0.16100628
[9] 0.17653450 0.23526415 0.18605374 0.28176760 0.21271178 0.18993928 0.23967917 0.10331625
[17] 0.06660912 0.14886864 0.08650808 0.08143249 0.11509542 0.10394732 0.09905027 0.09690067
[25] 0.10476192 0.09751349 0.14700768 0.07701766 0.08245111 0.10295656 0.13626823 0.13603139
[33] 0.09903021 0.06766919 0.08751213 0.08073908
[[11]][[2]]$y
[1] 0.1701724986 0.1208824123 0.2338729522 0.1209455779 0.3300957447 0.1706294193
[7] 0.1705313760 0.2332303919 0.2711884717 0.3552578530 0.2713047573 0.4697435079
[13] 0.3306241875 0.3306334156 0.3917919783 0.1206405404 0.0001517062 0.2092263075
[19] 0.0625377376 0.0626723921 0.1209466274 0.1206521300 0.1208254490 0.1200861740
[25] 0.1205284534 0.1200039232 0.2091607370 0.0623951050 0.0625294140 0.1208220512
[31] 0.1703381289 0.1706340778 0.1199836013 0.0004428609 0.0626036327 0.0626990573
[[11]][[2]]$yf
[1] 0.1704190203 0.1209248725 0.2335516721 0.1209248725 0.3303645801 0.1706294193
[7] 0.1704190203 0.2335516721 0.2711884717 0.3552578530 0.2713047573 0.4697435079
[13] 0.3306241875 0.3303645801 0.3917919783 0.1206937248 0.0001517062 0.2092263075
[19] 0.0626084467 0.0626084467 0.1209248725 0.1206937248 0.1206937248 0.1200245662
[25] 0.1206937248 0.1200245662 0.2091607370 0.0623951050 0.0626084467 0.1206937248
[31] 0.1704190203 0.1704190203 0.1200245662 0.0004428609 0.0626084467 0.0626084467
[[11]][[3]]
[[12]]
[[12]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 0.285612011 0.06975416
VRP_2_3 -0.240568520 0.15821396
VRP_3_2 -0.042333316 -0.06888741
VRP_1_2 0.206147707 0.03877824
VRP_1_3 0.019881485 -0.02432232
VRP_2_1 0.009749131 -0.03771493
VRP_2_2 0.083764172 -0.03097856
VRP_3_1 -0.275001651 -0.02511780
VRP_3_3 -0.047251020 -0.07972534
$centroids
PCoA1 PCoA2
1 0.198679780 0.03683953
2 0.007703531 -0.02387061
3 -0.061074290 -0.07096175
attr(,"class")
[1] "ordiplot"
[[12]][[2]]
[[12]][[2]]$x
[1] 0.53884609 0.36562165 0.15954177 0.30349773 0.31891641 0.25264980 0.57733887 0.37079417
[9] 0.30474945 0.47311718 0.33059891 0.33343202 0.38447495 0.21962059 0.31121476 0.29478240
[17] 0.12599723 0.14429100 0.17111566 0.27149518 0.06571064 0.22015673 0.24244383 0.16958518
[25] 0.49227249 0.30966095 0.15033082 0.14983360 0.31815367 0.13291410 0.12404711 0.30710632
[33] 0.15415775 0.37151625 0.18493099 0.27038578
[[12]][[2]]$y
[1] 0.991854111 0.645912391 0.148576224 0.513163915 0.537916810 0.393605495 1.030278490
[8] 0.647128790 0.513138030 0.907181053 0.546127015 0.647407253 0.692604501 0.394244339
[15] 0.516052551 0.514094333 0.146438839 0.145236419 0.256180517 0.390921134 0.004070923
[22] 0.392314015 0.396101232 0.257983261 0.903594413 0.514844340 0.144792588 0.148284564
[29] 0.517319407 0.149049761 0.148582720 0.526807345 0.143878783 0.646378927 0.256880205
[36] 0.390664595
[[12]][[2]]$yf
[1] 0.991854111 0.646659822 0.148576224 0.513465426 0.537916810 0.392975135 1.030278490
[8] 0.646753858 0.513465426 0.905387733 0.546127015 0.646659822 0.692604501 0.392975135
[15] 0.518755911 0.513465426 0.146609096 0.146609096 0.257014661 0.392975135 0.004070923
[22] 0.392975135 0.392975135 0.257014661 0.905387733 0.518755911 0.146609096 0.146609096
[29] 0.518755911 0.146609096 0.146609096 0.518755911 0.146609096 0.646753858 0.257014661
[36] 0.392975135
[[12]][[3]]
[[13]]
[[13]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 -0.0156069532 0.043682824
VRP_1_2 -0.0246628756 0.004058138
VRP_1_3 -0.0271403380 0.003502152
VRP_2_1 -0.0008647333 -0.019163972
VRP_2_2 -0.0142250170 -0.022871057
VRP_2_3 -0.0050351360 -0.021716490
VRP_3_1 0.0307112239 0.012382825
VRP_3_2 0.0311997678 0.007554697
VRP_3_3 0.0256240615 -0.007429117
$centroids
PCoA1 PCoA2
1 -0.023524336 0.012835024
2 -0.006362871 -0.021143717
3 0.029223573 0.004263319
attr(,"class")
[1] "ordiplot"
[[13]][[2]]
[[13]][[2]]$x
[1] 0.06205454 0.06395590 0.07041075 0.07311142 0.07472132 0.06908133 0.07137604 0.07988861
[9] 0.04612878 0.06109659 0.05989634 0.05709941 0.07277572 0.07054681 0.06393194 0.05880214
[17] 0.06434224 0.05752784 0.07376639 0.07297891 0.06770805 0.05025259 0.04892650 0.06367972
[25] 0.06342686 0.05806361 0.05297295 0.06919009 0.07338539 0.07068333 0.06648445 0.06001680
[33] 0.06641512 0.05773842 0.05945587 0.05803279
[[13]][[2]]$y
[1] 0.033025731 0.032860080 0.052392411 0.059054212 0.045955468 0.045233787 0.052863191
[8] 0.059349189 0.002708519 0.027425682 0.026898142 0.017142693 0.047765475 0.047407411
[15] 0.045923132 0.029920121 0.028170693 0.019444604 0.050113237 0.050018385 0.048631626
[22] 0.018801299 0.010968763 0.038994244 0.031681149 0.023572293 0.014893445 0.056904911
[29] 0.050431654 0.041938771 0.043344286 0.038675680 0.033096107 0.012310412 0.025070642
[36] 0.013156090
[[13]][[2]]$yf
[1] 0.032702060 0.035808851 0.049660876 0.051388643 0.051388643 0.046932706 0.050215684
[8] 0.059349189 0.002708519 0.032702060 0.027296302 0.015958090 0.050215684 0.049660876
[15] 0.035808851 0.027296302 0.035808851 0.015958090 0.051388643 0.050215684 0.046932706
[22] 0.015958090 0.010968763 0.035808851 0.032702060 0.023572293 0.015958090 0.049660876
[29] 0.051388643 0.049660876 0.043344286 0.032702060 0.035808851 0.015958090 0.027296302
[36] 0.015958090
[[13]][[3]]
[[14]]
[[14]][[1]]
$sites
PCoA1 PCoA2
VRP_3_2 0.008421582 -0.020936817
VRP_3_1 0.036652409 0.014538507
VRP_2_1 -0.002798301 -0.016604044
VRP_2_2 -0.002426286 -0.010846788
VRP_2_3 0.019729565 0.013083993
VRP_3_3 0.021374467 0.019081601
VRP_1_2 -0.008772172 -0.005553182
VRP_1_1 -0.090144852 0.011784855
VRP_1_3 0.017963588 -0.004548125
$centroids
PCoA1 PCoA2
1 -0.0094166049 -0.004990169
2 -0.0001451989 -0.010408218
3 0.0233550822 0.008994914
attr(,"class")
[1] "ordiplot"
[[14]][[2]]
[[14]][[2]]$x
[1] 0.05272550 0.02768870 0.02171031 0.04474436 0.04628545 0.04174695 0.10480862 0.03176626
[9] 0.05338931 0.04894645 0.03531657 0.03592956 0.05425628 0.12793842 0.03821837 0.01652633
[17] 0.04476590 0.05005200 0.02624037 0.09284249 0.03214721 0.04286230 0.04378378 0.03087416
[25] 0.09089354 0.02955082 0.03998968 0.04781716 0.11200956 0.03039168 0.05309800 0.11386331
[33] 0.03725078 0.08717123 0.04030081 0.11047826
[[14]][[2]]$y
[1] 1.172684e-04 4.545612e-05 3.159810e-05 1.231871e-04 1.222638e-04 9.337321e-05
[7] 1.369863e-01 6.113762e-05 1.354887e-04 1.265621e-04 7.878096e-05 4.144734e-05
[13] 1.648050e-04 1.371027e-01 6.980314e-05 1.409952e-05 1.123382e-04 1.259018e-04
[19] 4.794394e-05 1.369811e-01 6.636298e-05 1.117257e-04 1.208863e-04 6.182121e-05
[25] 1.369849e-01 5.923787e-05 3.917696e-05 1.178448e-04 1.370920e-01 6.379004e-05
[31] 1.439399e-04 1.371057e-01 6.248008e-05 1.369779e-01 9.648478e-05 1.370433e-01
[[14]][[2]]$yf
[1] 1.232441e-04 4.670003e-05 3.159810e-05 1.188039e-04 1.200543e-04 9.492900e-05
[7] 1.369863e-01 6.053337e-05 1.397143e-04 1.232441e-04 6.053337e-05 6.053337e-05
[13] 1.648050e-04 1.371042e-01 6.053337e-05 1.409952e-05 1.188039e-04 1.232441e-04
[19] 4.670003e-05 1.369830e-01 6.053337e-05 1.117257e-04 1.188039e-04 6.053337e-05
[25] 1.369830e-01 5.923787e-05 6.053337e-05 1.200543e-04 1.370920e-01 6.053337e-05
[31] 1.397143e-04 1.371042e-01 6.053337e-05 1.369779e-01 9.492900e-05 1.370433e-01
[[14]][[3]]
[[15]]
[[15]][[1]]
$sites
PCoA1 PCoA2
VRP_1_2 -0.026841301 0.011363264
VRP_1_3 -0.050267746 0.004659062
VRP_2_1 -0.024898063 -0.041060881
VRP_2_3 -0.017931278 -0.037613303
VRP_3_3 0.076104243 0.020811430
VRP_1_1 -0.102352036 0.045407972
VRP_2_2 0.008860332 -0.036968080
VRP_3_1 0.074477657 0.011570676
VRP_3_2 0.062848193 0.021829861
$centroids
PCoA1 PCoA2
1 -0.05447831 0.01560738
2 -0.01334609 -0.03829317
3 0.07135836 0.01888926
attr(,"class")
[1] "ordiplot"
[[15]][[2]]
[[15]][[2]]$x
[1] 0.08473959 0.10010231 0.08706934 0.12596937 0.12342978 0.09751500 0.13199633 0.11997764
[9] 0.08847274 0.09102040 0.14440484 0.10693615 0.10071408 0.14771231 0.12615928 0.06088207
[17] 0.12880186 0.12694224 0.08287255 0.12946614 0.11821071 0.11726885 0.12482286 0.06226351
[25] 0.11706713 0.11688490 0.18641492 0.10588247 0.07118373 0.05903746 0.14643744 0.18578713
[33] 0.17762483 0.10175621 0.09933862 0.07836007
[[15]][[2]]$y
[1] 0.002865975 0.120212246 0.119489171 0.124782631 0.124534967 0.120210190 0.126155844
[8] 0.122997093 0.119805140 0.119113290 0.127064808 0.121846390 0.119880800 0.128421592
[15] 0.125268338 0.001494094 0.124820669 0.124498345 0.003282155 0.124562687 0.123198429
[22] 0.123326622 0.125294220 0.002092996 0.123068967 0.121704336 0.218423008 0.121932121
[29] 0.001812466 0.001955569 0.127360661 0.219055196 0.216474679 0.121651778 0.120324017
[36] 0.003180639
[[15]][[2]]$yf
[1] 0.003109590 0.120156813 0.119469200 0.124871148 0.124534967 0.120156813 0.126155844
[8] 0.123174048 0.119469200 0.119469200 0.127064808 0.121827616 0.120156813 0.128421592
[15] 0.124871148 0.001724832 0.124871148 0.124871148 0.003109590 0.124871148 0.123174048
[22] 0.123174048 0.124871148 0.001952731 0.123068967 0.121827616 0.218739102 0.121827616
[29] 0.001952731 0.001724832 0.127360661 0.218739102 0.216474679 0.121651778 0.120156813
[36] 0.003109590
[[15]][[3]]
[[16]]
[[16]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 -0.12912773 0.014919557
VRP_1_2 -0.12398326 0.026363299
VRP_3_1 -0.04705503 -0.121009620
VRP_3_3 -0.10883998 0.042921314
VRP_1_3 -0.08709237 0.004051950
VRP_2_1 -0.05144528 -0.025468328
VRP_2_2 -0.08632816 -0.001723691
VRP_3_2 -0.11654287 0.048350178
VRP_2_3 0.75041469 0.011595341
$centroids
PCoA1 PCoA2
1 -0.11465395 0.01583922
2 -0.03914869 -0.01917113
3 -0.10382557 0.02363153
attr(,"class")
[1] "ordiplot"
[[16]][[2]]
[[16]][[2]]$x
[1] 0.10805227 0.18410319 0.13900472 0.11935255 0.14265616 0.12809462 0.12587721 0.88313342
[9] 0.19118181 0.13742821 0.11491675 0.15512800 0.12601363 0.14085309 0.87864655 0.18594097
[17] 0.14603310 0.12800543 0.15016857 0.19136278 0.80890973 0.10300059 0.12389418 0.11514055
[25] 0.08396771 0.86287654 0.10380084 0.08219937 0.10011870 0.83934294 0.10410117 0.13267105
[33] 0.80562158 0.11248810 0.83957518 0.87025116
[[16]][[2]]$y
[1] 0.12445152 0.15773938 0.05687559 0.09021877 0.08331357 0.09884692
[7] 0.06533217 361.46198517 0.24863556 0.06760507 0.08605588 0.15116373
[13] 0.09294472 0.06024447 361.42010756 0.19562993 0.16664327 0.09757719
[19] 0.16402046 0.20623136 361.36661211 0.06426585 0.10291695 0.07488416
[25] 0.01060460 361.44411066 0.07005978 0.01062040 0.07076438 361.38130382
[31] 0.06925300 0.11324580 361.38412162 0.08128672 361.37087866 361.44806846
[[16]][[2]]$yf
[1] 0.08638663 0.15989171 0.08638663 0.08638663 0.08638663 0.08638663
[7] 0.08638663 361.46198517 0.22743346 0.08638663 0.08638663 0.15989171
[13] 0.08638663 0.08638663 361.43742889 0.19562993 0.15989171 0.08638663
[19] 0.15989171 0.22743346 361.37536687 0.06751512 0.08638663 0.08638663
[25] 0.01061250 361.43742889 0.06965639 0.01061250 0.06751512 361.37609124
[31] 0.06965639 0.08638663 361.37536687 0.08638663 361.37609124 361.43742889
[[16]][[3]]
[[17]]
[[17]][[1]]
$sites
PCoA1 PCoA2
VRP_1_1 0.062107545 -0.037740411
VRP_1_2 -0.030214045 -0.029643538
VRP_1_3 0.086600042 0.007985490
VRP_2_1 0.004405502 -0.013286614
VRP_2_2 -0.072467053 -0.005408393
VRP_2_3 -0.047223862 -0.015288095
VRP_3_1 -0.075638046 0.037051825
VRP_3_2 0.069218605 0.035193772
VRP_3_3 0.003211311 0.021135965
$centroids
PCoA1 PCoA2
1 0.05646762 -0.02889193
2 -0.03755355 -0.01199711
3 0.00316067 0.02179559
attr(,"class")
[1] "ordiplot"
[[17]][[2]]
[[17]][[2]]$x
[1] 0.10162273 0.06591117 0.08198579 0.15089154 0.12650980 0.15726581 0.08923962 0.09646000
[9] 0.13255407 0.05650580 0.06870077 0.06765814 0.09440398 0.12207841 0.06961997 0.10034433
[17] 0.16533422 0.14665758 0.16966472 0.06267847 0.10175429 0.09618121 0.07806267 0.10842552
[25] 0.08804399 0.06176993 0.08667708 0.07764806 0.15421615 0.10740195 0.08475413 0.13932022
[33] 0.08187881 0.15570791 0.09741892 0.08432889
[[17]][[2]]$y
[1] 0.13775726 0.07310506 0.09550029 0.22878515 0.18595251 0.26668594 0.11517051 0.13899792
[9] 0.18623190 0.04959500 0.09219700 0.06492794 0.13845501 0.16893661 0.09491767 0.13700546
[17] 0.27784644 0.21705465 0.29512753 0.07264569 0.14639486 0.14084901 0.09065825 0.17128881
[25] 0.12235496 0.06935458 0.08452368 0.09322455 0.25256932 0.16298009 0.08075612 0.17769063
[33] 0.08279556 0.24807885 0.15244757 0.09612966
[[17]][[2]]$yf
[1] 0.14240343 0.07022623 0.09007809 0.22878515 0.18329168 0.26668594 0.11876273 0.13992346
[9] 0.18329168 0.04959500 0.09007809 0.07022623 0.13845501 0.17011271 0.09007809 0.14240343
[17] 0.27784644 0.21705465 0.29512753 0.07022623 0.14639486 0.13992346 0.09007809 0.17011271
[25] 0.11876273 0.06935458 0.09007809 0.09007809 0.25032409 0.16298009 0.09007809 0.18329168
[33] 0.09007809 0.25032409 0.14240343 0.09007809
[[17]][[3]]
[[18]]
[[18]][[1]]
$sites
PCoA1 PCoA2
VRP_3_3 0.06782801 -0.035330182
VRP_1_1 -0.06694854 0.061075726
VRP_1_2 -0.27099063 -0.023001237
VRP_1_3 0.03036859 0.011924289
VRP_2_1 0.05853868 0.040030489
VRP_2_2 0.02000853 0.030530311
VRP_2_3 0.08795823 -0.006333070
VRP_3_1 0.04167647 -0.001687456
VRP_3_2 0.03156066 -0.077208870
$centroids
PCoA1 PCoA2
1 -0.06803463 0.05416469
2 0.05647768 0.02881967
3 0.05339190 -0.03757433
attr(,"class")
[1] "ordiplot"
[[18]][[2]]
[[18]][[2]]$x
[1] 0.16867758 0.34231712 0.08175996 0.10328657 0.09825592 0.07098349 0.06099132 0.05891458
[9] 0.23163666 0.12998747 0.15847241 0.12368672 0.18318577 0.13921078 0.17583737 0.30822067
[17] 0.33681366 0.29896449 0.36128886 0.31519346 0.30869892 0.08469924 0.06261895 0.10047301
[25] 0.05348674 0.09869034 0.07269115 0.07451242 0.07266831 0.13228544 0.10561606 0.06351432
[33] 0.11658405 0.07221525 0.10359702 0.08203917
[[18]][[2]]$y
[1] 3.538298e-04 4.703164e-01 1.018733e-04 1.329529e-04 1.426967e-04 4.635069e-05
[7] 5.222287e-05 6.511205e-05 4.703218e-01 2.560678e-04 2.545198e-04 2.113881e-04
[13] 3.606985e-04 3.016353e-04 4.091406e-04 4.703422e-01 4.702439e-01 4.703120e-01
[19] 4.702702e-01 4.703156e-01 4.703525e-01 9.916011e-05 5.347813e-05 1.246869e-04
[25] 5.343880e-05 1.530809e-04 7.484154e-05 1.176250e-04 9.299083e-05 1.980623e-04
[31] 1.517025e-04 9.048402e-05 2.009512e-04 7.166414e-05 9.684349e-05 1.126251e-04
[[18]][[2]]$yf
[1] 3.538298e-04 4.703093e-01 1.078209e-04 1.300522e-04 1.300522e-04 6.841736e-05
[7] 5.693768e-05 5.693768e-05 4.703093e-01 2.270651e-04 2.780776e-04 2.113881e-04
[13] 3.849195e-04 2.780776e-04 3.849195e-04 4.703093e-01 4.703093e-01 4.703093e-01
[19] 4.703093e-01 4.703093e-01 4.703093e-01 1.078209e-04 5.693768e-05 1.300522e-04
[25] 5.343880e-05 1.300522e-04 8.391619e-05 1.078209e-04 8.391619e-05 2.270651e-04
[31] 1.517025e-04 6.841736e-05 2.009512e-04 7.166414e-05 1.300522e-04 1.078209e-04
[[18]][[3]]
[[19]]
[[19]][[1]]
$sites
PCoA1 PCoA2
VRP_2_2 -0.0266066570 -0.001924197
VRP_1_3 -0.0749825196 0.020006172
VRP_3_2 0.0569976754 -0.001395119
VRP_3_3 -0.0110483540 -0.063660496
VRP_1_2 -0.0496615022 -0.006473644
VRP_2_1 0.0110712512 -0.028139431
VRP_2_3 0.0007964805 0.027013331
VRP_3_1 0.0864768332 0.005205835
VRP_1_1 0.0069567926 0.049367548
$centroids
PCoA1 PCoA2
1 -0.047994013 0.014936042
2 -0.008175006 0.002042303
3 0.054854314 -0.007580292
attr(,"class")
[1] "ordiplot"
[[19]][[2]]
[[19]][[2]]$x
[1] 0.06631031 0.09417298 0.06999634 0.04539349 0.06281311 0.04943648 0.11823346 0.06468467
[9] 0.13784673 0.10595172 0.05677512 0.10423959 0.08714526 0.16533447 0.08314118 0.09540643
[17] 0.11538898 0.06834988 0.07555813 0.06105225 0.06915638 0.07585823 0.06423947 0.09748769
[25] 0.12168792 0.11471033 0.08035455 0.06546200 0.13994604 0.08423123 0.06700693 0.09464130
[33] 0.08574203 0.09525646 0.03660271 0.09281513
[[19]][[2]]$y
[1] 0.09175780 0.14068969 0.11679918 0.04817891 0.07961175 0.05406343 0.18689146 0.07840507
[9] 0.22666197 0.18691435 0.06468234 0.17065956 0.11447452 0.26296831 0.12428062 0.16532663
[17] 0.18748799 0.09036588 0.11695703 0.06263536 0.12249024 0.12223201 0.07934168 0.15859967
[25] 0.22766688 0.18366512 0.11540909 0.09679543 0.23506534 0.11776883 0.09641360 0.15102668
[33] 0.11831314 0.14849529 0.02551281 0.14303752
[[19]][[2]]$yf
[1] 0.09383318 0.14186361 0.11874718 0.04817891 0.07911950 0.05406343 0.18718972 0.07911950
[9] 0.22716443 0.18528973 0.06365885 0.17065956 0.11874718 0.26296831 0.11874718 0.16196315
[17] 0.18718972 0.09383318 0.11874718 0.06365885 0.11874718 0.11874718 0.07911950 0.16196315
[25] 0.22716443 0.18528973 0.11874718 0.09383318 0.23506534 0.11874718 0.09383318 0.14976098
[33] 0.11874718 0.14976098 0.02551281 0.14186361
[[19]][[3]]
Remove dissimilar replicates
Based on the output from 04-filter-ASV-by-SODM.Rmd, I now want to filter the dataset to remove replicates for loci that have high dissimilarity values, listed here: /data/reference_pool_dissimilarity_samples_to_remove.csv.
# bind together the vouchered and full reference SODM dataframes
reference_df_sodm_filtered <- vrp_sodm_filtered_df %>% bind_rows(frp_sodm_filtered_df)
A clean, non-redundant version of the reference sample dataframe
ref_sodm_filtered_unique <- reference_df_sodm_filtered %>%
select(locus, seq, sample, count) %>%
unique() %>% # if there are multiple entries with different counts, we want to collapse those reads
group_by(locus, seq, sample) %>%
mutate(total_reads = sum(count)) %>%
select(-count) %>%
rename(count = total_reads)
So that is the dataframe from which we want to remove this particular list of locus-samples
# read in the list of samples to remove
tossers <- read_csv("../data/reference_pool_dissimilarity_samples_to_remove.csv")Parsed with column specification:
cols(
locus = [31mcol_character()[39m,
sample = [31mcol_character()[39m
)It turns out that an anti-join is all I need for this filtering step.
ref_sodm_bray_filtered_unique <- ref_sodm_filtered_unique %>%
anti_join(., tossers, by = c("locus", "sample"))
Okay, so that is the dataset that I can work through the assessment analyses with, beginning with summary statistics, then adding in the taxonomy and assessing true/false positives in the vouchered samples and breadth of taxonomic coverage in the full reference pool.
Save filtered dataframe
Save the filtered feature table output from occupancy modeling and dissimilarity
# save this version of the feature table to combine with taxonomy for locus-integrated taxonomy
ref_sodm_bray_filtered_unique %>%
saveRDS("../data/feature_table_sodm_bray_filtered.rds", compress = "xz")
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